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 .
Second Non-Final Office Action
The instant office action is a second non-final office action superseding the previous non-final office action in view of a rejection not necessitated by amendment.
Status of the Claims
Claims 1-20 are pending and examined herein.
No claims are canceled.
Priority
As detailed on the 03 July 2023 filing receipt, the application claims priority as early as 10 March 2016. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Withdrawn Objections and/or Rejections
The claim objections from the previous office action are withdrawn in view of amendment of terms to be internally consistent and article-noun plurality agreement.
The claim rejections under 35 USC 112(b) are withdrawn in view of amendment clarifying terminology and required list elements.
The rejection under 35 USC 103 is withdrawn in view of persuasive argument, which explain the applied art, namely Berglund (Protein Science 17: 606-613, 2007; previously cited on the 13 March 2026 PTO-892 form) and Kanduc (Current Pharmaceutical Design 14: 289-295, 2008; previously cited on the 16 February 2023 IDS form) teach away from the instant use of pentamers with high similarity to the host proteome, where Berglund teaches similarity below a threshold (pg. 612, col. 1, second paragraph) and Kanduc teaches no/low similarity matches (pg. 289, col. 1, third paragraph). Therefore, high similarity as required by the claims is not taught and thus the claims are interpreted as free of the prior art.
The following rejections are the complete set of rejections applied to the instant claims.
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-20 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.
Claim 1 recites “the host proteome” but the term “host proteome” is not previously introduced. Therefore, the term lacks clear antecedence with respect to the host protein. Dependent claims are rejected on similar grounds.
Claims 18-19 recite “the human proteome” but the term “human proteome” is not introduced in parent claim 1. Therefore, the term lacks clear antecedence. To overcome this rejection, the claim could be amended to recite “a human proteome” or to depend on claim 2, where a human proteome is introduced. This rejection is not in view of amendment and thus necessitated a second non-final office action.
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 1-20 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 identifying epitope mimics.
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, 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)).
The independent claim recites assigning curation, which are interpreted as mental steps of listing proteins and their functions, which the human mind is practically equipped to perform.
The independent claim recites computing probable epitopes in each protein. This claim is interpreted as reciting a metric of probability, which requires a mathematical calculation to determine, and thus is considered to be a mathematical concept. Computing whether something is probable or not is interpreted as requiring calculating probability. Subsequent claims recite ranking the probability of epitopes also suggests a number being calculated, supported by the disclosure of BEPI probability numerically in the specification (e.g., Table 9). Alternatively, strictly comparing matches between a sequence query and reference, where matches suggest probability, would be a mental process of sequence alignment.
The independent claim recite identifying the core peptide, where a core peptide is defined in the specification as the central five amino acids in a nine amino acid sequence (pg. 25, lines 10-13). The human mind is practically equipped to evaluate which five amino acids are the central ones in a string of nine.
The independent claim recites computing probable epitopes for a protein of interest, which is interpreted as a mathematical concept for the reasons explained above.
The independent claim recites identifying the core peptide of the query sequence, which is interpreted as a mental process for the reasons explained above.
The independent claim recites comparing core peptides in the database and query, where comparing sequence data is a step the human mind is practically equipped to perform as data evaluation or judgment.
The independent claim recites identifying peptides that are identical in the database and query core peptides, which is a more specific data evaluation or judgment as explained above and thus a mental process.
The independent claim recites identifying the function of the host proteins, which is interpreted as referencing the protein database, which is a step the human mind is practically equipped to perform.
Claims 2-3 recite additional information about the data assembled in the database, where data is a non-statutory category and thus interpreted as abstract.
Claim 4-7 recite additional information about the metric for selection of probable B cell epitopes, where a criterion for selection is interpreted as related to selection, which the human mind is practically equipped to perform.
Claims 8-9 recite additional data about the epitope evaluation of the epitopes from the database and query, where data is a non-statutory category and thus interpreted as abstract.
Claim 10 recites using keywords to search a database, where searching a database by keyword is a step the human mind is practically equipped to perform.
Claims 11-16 recite additional information about using keywords and the keywords themselves for searching a database, and so are considered additional details about the mental process described above.
Claim 17 recites analyzing alternative sequences and identifying alternative sequences, where analyzing and identifying sequences are steps the human mind is practically equipped to perform.
Claim 18 recites analyzing a biopharmaceutical, identifying epitope mimics, and preparing a report. Analyzing and identifying epitopes are abstract ideas for the reasons explained above. Preparing a report is interpreted as including, under a broadest reasonable interpretation, mental steps before production of a physical report and as such may be interpreted as a mental process.
Claim 19 recites determining identical matches by comparison with homologous proteins, where determining matches is previously discussed as a mental process of data evaluation which the human mind is practically equipped to perform. Claim 19 further recites selecting an animal model, where making a selection is a mental step the human mind is practically equipped to perform.
Claim 20 recites identifying mimics, which is a mental process for the reasons described above.
Thus, the claims recite abstract ideas and thus must be examined further to determine whether elements in addition to the abstract ideas integrate the judicial exceptions 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))?
Because the claims recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they recite elements in addition to the abstract ideas which integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(III)).
The independent claim recites additional elements that are not abstract ideas: "a computer readable medium,” “entering a sequence… into a computer,” and assembling databases. The dependent claims also recite “providing a synthetic protein,” “contacting said synthetic protein with serum,” and identifying the presence of antibodies (claim 20).
The elements of using a non-transitory computer readable medium and a computer itself are interpreted as using a general purpose computer to perform the abstract steps, which does not integrate the abstract idea into a practical application (MPEP 2106.05(f)).
Assembling a database, whether based on all proteins in a host proteome or of core proteins, is interpreted as using storing data, which is preparatory step related to data gathering and thus insignificant extra-solution activity which does not integrate the abstract idea into a practical application (MPEP 2016.05(g)). The database, if electronic, may also be considered to be use of a general purpose computer storing data (MPEP 2106.05(f)).
Meanwhile, the steps of providing a synthetic protein, contacting it with serum from a subject, and identifying the presence of antibodies are interpreted as instructions to apply the abstract ideas (MPEP 2106.05(f)). It is not clear than an improvement is asserted, a treatment is administered, or a transformation is occurring.
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: 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). The claims recite the following additional elements that are not abstract ideas: "a computer readable medium” (claim 1), “entering a sequence… into a computer,” (claim 1), assembling databases (claim 1), “providing a synthetic protein” (claim 20), “contacting said synthetic protein with serum” (claim 20), and identifying the presence of antibodies (claim 20).
Entering data into a computer with memory is interpreted as receiving or transmitting information using a computer, which is a conventional computer task (buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014); MPEP 2106.056(d)).
Storing data in a database is a conventional computer function (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93) ); MPEP 2106.056(d)).
Doores (Chemistry: A European Journal 12(3): 656-665, 2006; previously cited on the 13 March 2026 PTO-892 form) teaches analysis of a synthetic epitope mimic to validate a mimic selection process (pg. 662, col. 1, first paragraph), which involves contact with the serum and antibody detection.
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 15 June 2026 Applicant Remarks
Applicant remarks state “a method that computes B cell epitopes across an entire host
proteome and assembles and queries a proteome-scale core-peptide database in computer-readable
memory is not a process that can be practically performed in the human mind” and evaluation on an element-by-element basis is improper dissection into individual steps (pg. 7, third paragraph). It is unclear how this interpretation can be a proper understanding of 101 analysis, as individual elements are considered to determine if they are abstract ideas or elements in addition to the abstract ideas at Step 2A Prong 1, then elements in addition to the abstract ideas are more specifically analyzed at Steps 2A Prong 2 and 2B.
Applicant remarks state the number of proteins in the human proteome precludes the comparisons from being a mental process (pg. 7, third paragraph). This argument is unpersuasive for two reasons. First, repetitive analysis of multiple sequences does not preclude a step from being a mental process. While it is acknowledged that such computations performed mentally, or with paper and pencil, would take considerable time and effort, the singular purpose of computers and computer networks, to perform large numbers of calculations via algorithms, rapidly, and without error (assuming no error in user input). Although a general-purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same and constitutes an abstract idea. See Bancorp Serves., L.L.C. v. Sun life Assur. Co. of Canada (U.S.), 687 F.3d 1266, 1278 (Fed. Cir. 2012) (holding that "the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter"); see also SiRF Tech., Inc. v. lnt'I Trade Comm'n, 601 F.3d 1319,1333 (Fed. Cir. 2010) (holding that: In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations). Second, at least the independent claims do not require a human proteome, so the remarks are not commensurate in scope with the claims.
Applicant remarks state computing probable B cell epitopes is not a mathematical concept (pg. 7, fourth paragraph). Computing whether something is probable or not is interpreted as requiring calculating probability, supported by the disclosure of BEPI probability numerically in the specification (e.g., Table 9).Alternatively, strictly comparing matches between a sequence query and reference, where matches suggest probability, would be a mental process of sequence alignment. In either case, this step is an abstract idea.
Applicant remarks state the claims’ recited judicial exceptions are integrated into a practical application in the form of an improvement (pg. 7, last paragraph to pg. 8, first paragraph). This argument is therefore considered to be directed to Step 2A Prong Two of 101 analysis. The claims are considered to be directed to comparing sequences and storing the sequences electronically in databases. The alleged improvement therefore appears to be based on comparing the k-mer within sequences to detect epitope mimics and not storing sequences in a database. The database, which may be considered an element in addition to the abstract ideas, is not improved by virtue of the data being stored in it. The analogy between the instant claims and Ex Parte Desjardins, for example, is not persuasive because in the latter, the computer-technology is what is being improved, particularly catastrophic forgetting, whereas in the instant claims, the improvement is to epitope mimic detection, which is a biochemical problem.
Applicant remarks state the database storing the information is an integral part of the invention and not insignificant extra-solution activity (pg. 8, second paragraph). For similar reasons as above, storing information on a database or accessing a database are tangential to the comparison and identification steps. As explained in the remarks (pg. 8, second paragraph), the comparing and identifying steps rely on the data collection steps and storage to perform the abstract ideas, which is why they are interpreted as data gathering and/or application using a general purpose computer.
Therefore, the rejection under 35 USC 101 is maintained.
Conclusion
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/Robert J. Kallal/Examiner, Art Unit 1685
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