DETAILED ACTION
Applicant's request for continued examination, filed 12/29/2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/29/2025 has been entered.
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copy has been filed in the Instant Application No. 17/552,861, filed on 2/8/2022.
Claim Status
Claims 1-2 and 6-7 are pending.
Claims 3-5 are cancelled.
Claims 1-2 and 6-7 are rejected.
Claim Rejections - 35 USC § 101
Response to Amendment
In view of applicant’s amendments to the claims, previous rejections under 35 U.S.C. 101 have been reviewed, updated, and provided below.
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 1-2 and 6-7 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more. The claims recite a computer system and a method that supporst design for the artificial improvement of biological functions through data acquisition and computing co-occurrences. The judicial exception is not integrated into a practical application, said application is either generically recited computer elements that do not add a meaningful limitation to the abstract idea or it is insignificant extra solution activity and simply implementing the abstract idea on a computer. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the computer elements only store and retrieve information in memory as well as perform basic calculations that are known to be well-understood, routine and conventional computer functions as recognized by the decisions listed in MPEP § 2106.05(d).
Framework with which to Analyze Subject Matter Eligibility:
Step 1: Are the claims directed to a category of statutory subject matter (a process,
machine manufacture, or composition of matter)? [see MPEP § 2106.03]
Claims are directed to stator subject matter, specifically systems and methods (claims 1-2 and 6-7).
Step 2A Prong One: Do the claims recite a judicially recognized exception, i.e., an abstract idea, a law of nature, or a natural phenomenon? [see MPEP § 2106.04(a)]
The claims herein recite abstract ideas, mental processes and mathematical concepts.
With respect to the Step 2A Prong One evaluation, the instant claims are found herein to recite abstract ideas that fall into the grouping of mental processes and mathematical concepts.
Claims 1 and 7: Registering a history of the design, searching a database based on the pair information, building a table by extracting a gene other than the target gene, and evaluating the candidate gene, are processes of making a mental note, looking through a database, identifying/selecting information, and comparing/contrasting information that can be done with pen and paper or within the human mind and are therefore abstract ideas, specifically mental processes. Computing a co-occurrence number is a verbal articulation of a mathematical process and is therefore an abstract idea, specifically a mathematical concept.
Claim 2: The biological resource being an artificial microorganism is merely further limiting the data itself, which is an abstract idea, specifically a mental process.
Claim 6: Summing the number of co-occurrences is a verbal articulation of a mathematical process and is therefore an abstract idea, specifically a mathematical concept. Evaluating the plurality of genes based on the computed sum is a process of comparing/contrasting information that can be done with pen and paper or within the human mind and is therefore an abstract idea, specifically a mental process.
Step 2A Prong Two: If the claims recite a judicial exception under prong one, then is the judicial exception integrated into a practical application? [see MPEP § 2106.04(d) and MPEP § 2106.05(a)-(c) & (e)-(h)]
Because the claims do recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application.
The following claims recite the following additional elements in the form of non-abstract elements:
Claim 1: A computer system, controller, program, and memory are all generic and nonspecific elements of a computer that do not improve the functioning of any computer or technology described herein [See MPEP § 2106.04(d)(1) and MPEP § 2106.05(d)].
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? [see MPEP § 2106.05]
Because the additional claim elements do not integrate the abstract idea into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept.
The claims do not recite additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are generic, conventional or nonspecific. These additional elements include:
The additional elements of a computer system, controller, program, and memory are generic and nonspecific elements of a computer that are well-understood, routine and conventional within the art and therefore do not improve the functioning of any computer or technology described therein (See Receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), Performing repetitive calculations, Flook, 437 U.S. at 594, 198 USPQ2d at 199 (recomputing or readjusting alarm limit values), and Storing and retrieving information in memory, Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015)) [See § MPEP 2106.05(d)(II)]. Therefore, taken both individually and as whole, the additional elements do not amount to significantly more than the judicial exception by providing an inventive concept.
Therefore, claims 1-2 and 6-7, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant's arguments filed 12/29/2025 have been fully considered but they are not persuasive. Applicant asserts that claims 1 and 7 are directed to patent-eligible subject matter, specifically that claim 1 sets forth an improvement to technology; the technological improvement being the improvement of an artificial microorganism. However, as examiner previously stated in the previous office action and in MPEP 2106.05(a) “It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements” and in section II of MPEP 2106.05(a) “To show that the involvement of a computer assists in improving the technology, the claims must recite the details regarding how a computer aids the method, the extent to which the computer aids the method, or the significance of a computer to the performance of the method. Merely adding generic computer components to perform the method is not sufficient”. Further, applicant asserts that the improvement can be provided by the additional element(s) in combination with the recited judicial exception. However, examiner reminds applicant that the additional elements cannot be generic, conventional, non-specific additional elements, but rather that some part of the additional elements needs to be an improvement – “Merely adding generic computer components to perform the method is not sufficient”.
Claim Rejections - 35 USC § 102
Response to Amendment
In view of applicant’s amendments to the claims previous rejections under 35 U.S.C. 102 have been reviewed, updated, and provided below.
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1 and 7 are rejected under 35 U.S.C. 102(a)(I) and (a)(II) as being anticipated by Toyoda et al. (US 20090112850 A1; previously cited).
Claim 1 is directed to a computer system which registers history of designs, searches databases, acquires additional information, computes correlations between the additional information and a related element, and evaluates the additional information based upon the correlation.
Claim 7 is directed to a method which registers history of designs, searches databases, acquires additional information, computes correlations between the additional information and a related element, and evaluates the additional information based upon the correlation.
Toyoda et al. teaches in the abstract “…a bio-item searching apparatus searches for a target bio-item with a keyword input by a user… the storage device stores a bio-item literature set having a literature in which the bio-item name is described for each of bio-items… control device searches each of the bio-item literature sets with the keyword to acquire the number (Nh) of literatures including the keyword for each of the bio-items, selects the bio-item in which the number-of-literatures Nh is 1 or larger as a candidate bio-item… calculates a correlation score between the bio-item and the keyword based on statistical calculation by using the number-of-literatures table for each of the candidate bio-items, and outputs the candidate bio-items to the output device based on the correlation score”, in paragraph [0001] “prioritizes and searches for "bio-items" such as a gene, a polymorphism, an affection, a medical agent, a bio-resource, a protein, a person, a group, an organization, a compound, a technical term, and a literature folder, and information related to the bio-items in an information processing field such as biology”, and in paragraph [0002] “searches a literature set with a keyword specified by a user to acquires a bio-item (hereinafter, a gene will be taken as an example) related to the keyword from the searching result, a method of calculating correlation scores between literatures and the keyword, ranking the literatures, and then displaying gene-related terms described in the literatures is used”, in paragraph [0003] “As a method for finding a promising gene closely related to the keyword, Patent Document 1 discloses a method for estimating a gene correlation from timings of expression of the genes. Patent Document 2 discloses an apparatus that performs link-searching for searching for objects connecting end-point keys, prioritizes the genes, takes in and searches for promising genes in a plurality of genes, and shows the promising genes with priorities”. Toyoda et al. further teaches in paragraph [0032] “The means for storing these data objects can be stored and read as structures, files, or records on a general storage medium such as a hard disk in addition to a memory. In the case of a structure on a memory, reading is performed via a pointer or reference to the structure…In the case of a record, the table name, primary key, and reference key are specified…”. A correlation is a measure describing a relationship where two variables change together, which would be synonymous with a co-occurrence number as indicated within the specification, and a morpheme is merely a similar or variant gene or region of the genome. Therefore, these definitions in view of the above citations from Toyoda et al. read on a computer system comprising a controller that executes a program recorded in a memory, wherein the controller is configured to: register a history of the design, wherein the history of the design includes pair information of a target gene or the biological resource and an operation on the target gene; search a database based on the pair information to extract a list of related documents including the pair information, the related documents are documents in which morphemes of the target gene and the operation exist; build a table by extracting a gene other than the target gene from the list of related documents as a candidate gene for improving the function of the biological resource and adding the candidate gene to the table; compute a co-occurrence number of the candidate gene co-occurring with the target gene based on the list of related documents, the co-occurrence number indicating the number of related documents in which both the target gene and the candidate gene exist; and evaluate the candidate gene based on the co-occurrence number.
Response to Arguments
Applicant's arguments filed 12/29/2025 have been fully considered but they are not persuasive. Applicant asserts that Toyoda et al. does not teach searching a database based on the pair information along with the teachings of the amended claims. However, as per Toyoda et al. paragraph [0003] “…performs link-searching for searching for searching for objects connecting end-point keys, prioritizes the genes, takes in and searches for promising genes in a plurality of genes…” and in paragraph [0032] “storing these data objects can be stored and read as structures…In the case of a record, the table name…”. Additionally, Toyoda et al. teaches that the genes are variants, paragraph [0004] “…a combination of two or more SNP sites showing a high correlation…”.
Claim Rejections - 35 USC § 103
Response to Amendment
In view of applicant’s amendments to the claims previous rejections under 35 U.S.C. 103 have been reviewed, updated, and provided below.
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.
Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Toyoda et al. (US 20090112850 A1; previously cited) as applied to claims 1 and 7 above, and further in view of SynBioHob Documentation (Web Page (2018) 1-15; previously cited).
Toyoda et al. teaches the method of claim 1 as previously described. Toyoda et al. also teaches in paragraph [0003] “an apparatus that performs link-searching for searching for objects connecting end-point keys, prioritizes the genes, takes in and searches for promising genes in a plurality of genes, and shows the promising genes with priorities”.
Toyoda et al. does not teach the biological resource as an artificial microorganism.
The SynBioHub documentation teaches on page 1 “SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources”, reading on wherein the biological resource is an artificial microorganism.
It would have been obvious at the time of the effective filing date of the invention to a person skilled in the art to combine the teachings of Toyoda et al. for the system and method of claims 1 and 7 with the teachings of the SynBioHub documentation that is a design repository and search engine for synthetic biological parts and constructs and the SynBioHub documentation points out on page 2, paragraph 2 “The adoption and use of SynBioHub, a community-driven effort, has the potential to overcome the reproducibility challenge across laboratories by helping to address the current lack of information about published designs”. One would have had a reasonable expectation of success given that both Toyoda et al. and SynBioHub have implemented relatively the same features and the only major difference seems to be the focus on synthetic (or artificial) biologics for SynBioHub. Therefore, it would have been obvious to one with ordinary skill in the art to incorporate the teachings of each and to be successful.
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Toyoda et al. (US 20090112850 A1; previously cited) as applied to claims 1 and 7 above, and further in view of Larson et al. (BMC Bioinformatics (2015) 1-17; previously cited).
Claim 6 is directed to the system of claim 5 and thus claim 1, but further specifies the adding of correlations with each of the plurality of genes and evaluating the plurality of candidate genes based upon the summed correlation.
Toyoda et al. teaches the system of claims 1 and 7 as previously described.
Larson et al. teaches on page 4, column 2, paragraph 3 “our linear statistic is motivated by trying to approximate the JG statistic, which is a sum of t statistics. Ackermann and Strimmer found little difference between summing correlations and summing t-statistics”, which is used to determine if there is a significant difference between the means of two groups, which reads on sum the number of co-occurrences of the candidate gene with each of the plurality of target genes; and evaluate the plurality of candidate genes based on the sum.
It would have been obvious at the time of the effective filing date of the invention to a person skilled in the art to combine the teachings of Toyoda et al. for the system and method of claims 1 and 7, with the teachings of Larson et al. for the summing of correlations and evaluations based upon said summed correlations, as they would effectively provide a pseudo t-test between what is being compared (in this case genes and candidate genes), i.e. showcasing whether or not there is a difference between the two groups. One would have had a reasonable expectation of success given that the method is merely adding up something that is already being calculated and Larson et al. not only provides a basis but also links to previous research who have used such methods. Therefore, it would have been obvious to one with ordinary skill in the art to incorporate the teachings of each and to be successful.
Response to Arguments
Applicant's arguments filed 12/29/2025 have been fully considered but they are not persuasive. Applicant asserts that Toyoda et al. does not read on claims 1 and 7 under 35 U.S.C. 102 as previously described and as such said deficiencies are not cured by previously cited 35 U.S.C. 103 prior art. However, as previously described above, Toyoda et al. is not deficient.
Conclusion
All claims are identical to or patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/K.N.A./ Examiner, Art Unit 1687
/OLIVIA M. WISE/ Supervisory Patent Examiner, Art Unit 1685