DETAILED ACTION
Applicant's request for continued examination, filed 4/16/2026, 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 4/16/2026 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 supports 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 the selected target genes as pair information, 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:
Claims 1 and 7: 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)]. Displaying a first graphic user interface, receiving a selection of one or more target genes, and displaying a second graphic user interface are insignificant extra solution activities, specifically mere data gathering and necessary data outputting (See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering)) [See MPEP § 2106.05(g)].
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.
The additional elements of displaying a first graphic user interface, receiving a selection of one or more target genes, and displaying a second graphic user interface are insignificant extra solution activities, specifically mere data gathering and necessary data outputting (See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering)) [See MPEP § 2106.05(g)]. 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 4/16/2026 have been fully considered but they are not persuasive.
Applicant asserts on page 7 of the Remarks filed 4/16/2026 that the independent claims 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”.
Applicant asserts on page 8 of the Remarks filed 4/16/2026 that claim 1 recites additional elements which provide the improvement to technology. 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”. The newly recited claim limitations are merely necessary data outputting and data gathering which have been previously identified by the court as insignificant extra solution activity under both Step 2A Prong Two and Step 2B. The use of a computer in this regard is merely as conveyance of the information, but does not transform the information or perform a process by which a human mind could not.
Applicant asserts on page 9 of the Remarks filed 4/16/2026 that the pair information recited in the claim is not an abstract concept that can be processed in the human mind but a structured representation. However, in paragraph [0019] of the specification the pair information is described as merely information of a gene and information regarding the modification of said gene “includes a plurality of pieces of pair information of a gene (related element) and an operation for the gene in the biological resource. The operation includes an operation for modifying a gene in order to improve a property, characteristic, performance, function, or attribute of a biological resource, and specific examples thereof include introduction of a new gene, enhancement of an existing gene, suppression thereof, and disruption thereof to a high-productivity microorganism”. This information is not a transformation of the information into something that is not understandable by the human mind but is rather the opposite; there is nothing to suggest within the specification that the information regarding the gene and the modifications of the gene which comprise the pair information is not understandable by the human mind as paragraph [0030] explains “the controller extracts pair information of a gene name and an operation name for the gene name as search information from each of the plurality of modification lists, and sequentially outputs a search query based on the pair information to the search document database & search engine…The related document is a document in which morphemes of "target gene name" of pair information and "operation name" of the pair information exist”.
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 withdrawn.
Response to Arguments
Applicant's arguments filed 4/16/2026 have been fully considered and they are persuasive. Specifically, applicant is asserts that the cited reference Toyoda et al. does not teach the newly recited limitations of the independent claims regarding user interfaces and displaying information. Examiner agrees and withdraws the rejections of the independent claims 1 and 7 under 35 U.S.C. 102.
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.
Claims 1-2 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Toyoda et al. (US 20090112850 A1; previously cited) and SynBioHub Documentation (Web Page (2018) 1-15; 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 the selected one or more target genes in association with the selected operation of the target gene in the tree structure as pair information; 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.
The SynBioHub documentation teaches on page 3, paragraph 1 “SynBioHub provides computational access for software and data integration, and a graphical user interface that enables users to search for and share designs…SynBioHub contains an interface for users to upload new biological data to the database,to visualize DNA parts, to perform queries to access desired parts, and to download SBOL, GenBank, FASTA, etc.”, on page 9, paragraph 2 “A Module, basically represents a grouping of structural and functional entities in a biological design… Just below the clickable options, the VisBol navigator is located, which displays the structure of that particular module. VisBOL is a Web based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format…The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL)version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL Navigator also has zooming capabilities. This, graphically represents the structure of the module. By hovering your pointer over this structure, you can view the following attributes of that particular module i.e, type of resource, identifier, name and role of the module”, reading on display, on the display, a first graphic user interface indicating a tree structure, as a data structure, of a design history database, the tree structure having a parent strain as a root and a plurality of modification generations as branches from the root, receive a selection of one or more target genes for the biological resource from the tree structure of the design history database in the first graphic user interface, display, on the display, a second graphic user interface showing the selected one or more target genes and receiving a selection of an operation on the one or more target genes via the second graphic user interface.
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, search engine, and user interface for synthetic biological parts and constructs as 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”. Furthermore, any changes in the user interface between the prior art and instant application are merely obvious optimizations of a finite number of identified predictable solutions for providing information within a UI> 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 2 is directed to the system of claim 1 but further specifies that the biological resource is an artificial microorganism.
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.
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Toyoda et al. (US 20090112850 A1; previously cited) and SynBioHub Documentation (Web Page (2018) 1-15; 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. and the SynBioHub Documentation teach 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. and the SynBioHub Documentation 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 4/16/2026 have been fully considered but they are not persuasive. Applicant asserts that in view of the amended claims the cited prior art is deficient under 35 U.S.C. 102 and as such the dependent 103 should be withdrawn. However, examiner reminds applicant that while the art may be deficient in regards a rejection under 35 U.S.C. 102, that does not mean it is deficient under 35 U.S.C. 103. As such the prior art, as provided above, provides for a prima facie case of obviousness under 35 U.S.C. 103 as outlined above.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEENAN NEIL ANDERSON-FEARS whose telephone number is (571)272-0108. The examiner can normally be reached M-Th, alternate F, 8-5.
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/K.N.A./ Examiner, Art Unit 1687
/LARRY D RIGGS II/ Supervisory Patent Examiner, Art Unit 1686
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