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 .
Change of Examiner
Please note that the Examiner of record has changed. All future responses should be addressed to Primary Examiner Pablo S. Whaley, USPTO, Art Unit 3619.
Election/Restriction
Applicant's election with traverse of Group II (claim 5), filed 05/11/2026, is acknowledged. Applicant argues that Groups I, II, and III share the same special technical feature and that no prior art has been cited. In response, contrary to applicant’s assertion, the examiner identified the special technical feature and prior art was indeed cited in the restriction requirement mailed 03/10/2026 (see page 5). As such, the Groups are still deemed to lack unity of invention for reasons set forth in the restriction because they are not so linked as to form a single general inventive concept under PCT Rule 13.1. In addition, Applicant has not submitted any evidence to the contrary. In response to applicant’s arguments regarding classification, applicant is reminded that this case was being analyzed under PCT Rules. Accordingly, the restriction is maintained. The requirement is still deemed proper and is therefore made FINAL. Claim 1-4 and 6 are hereby withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected inventions, there being no allowable generic or linking claim.
Rejoinder Comment
The examiner has required a restriction between apparatus/device and process/program claims to begin prosecution. Where the elected apparatus/device claims are subsequently found allowable, withdrawn process claims that depend from or otherwise require all the limitations of the allowable apparatus/system claim will be considered for rejoinder. All claims directed to a nonelected process/program invention must require all the limitations of an allowable apparatus/device claim for that process/program invention to be rejoined.
Status of Claims
Claims 5 and 7-9 are under examination.
Claims 7-9 are newly added via amendment.
Claims 1-4 and 6 are withdrawn.
Priority
Applicant' s claim for the benefit of priority under 35 U.S.C. 119(a)-(d) is acknowledged. This application is the National Stage filing under 35 USC 371 of PCT/JP2022/020744, filed on 05/18/2022. Receipt is acknowledged of papers submitted under 35 U.S.C. 119(a)-(d), which papers have been placed of record in the file. Accordingly, the effective priority date for the instant application is 05/18/2022.
Information Disclosure Statement
The two (2) information disclosure statement (IDS) document(s) submitted are in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS document(s) has/have been fully considered by the examiner.
Drawings
The drawings filed 11/17/2023 are acceptable.
Objections
The specification is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. See at least [0017, 0018, 0042]. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code. See MPEP § 608.01.
The specification is objected to as it contains non-standard section headings. See 37 CFR 1.77(b). For example, the specification recites a section entitled “Citations List , Non Patent Literature” [see page 1] and another section entitled “Supporting Information” [starting on page 18], and “Reference Signs List” [page 111]. Applicant is reminded that the listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, applications, or other information submitted for consideration by the Office, and MPEP § 609.04(a), subsection I. states, “the list may not be incorporated into the specification but must be submitted in a separate paper.” Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
In order to overcome this objection, a substitute specification should be provided that corrects above issues. The following guidelines illustrate the preferred layout for the specification of a utility application. These guidelines are suggested for the applicant' s use.
As provided in 37 CFR 1.77(b), the specification of a utility application should include the following sections in order. Each of the lettered items should appear in upper case, without underlining or bold type, as a section heading. If no text follows the section heading, the phrase “Not Applicable” should follow the section heading:
Content of Specification
(a) TITLE OF THE INVENTION: See 37 CFR 1.72(a) and MPEP § 606. The title of the invention should be placed at the top of the first page of the specification unless the title is provided in an application data sheet. The title of the invention should be brief but technically accurate and descriptive, preferably from two to seven words. It may not contain more than 500 characters.
(b) CROSS-REFERENCES TO RELATED APPLICATIONS: See 37 CFR 1.78 and MPEP § 211 et seq.
(c) STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT: See MPEP § 310.
(d) THE NAMES OF THE PARTIES TO A JOINT RESEARCH AGREEMENT. See 37 CFR 1.71(g).
(e) INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ON A READ-ONLY OPTICAL DISC, AS A TEXT FILE OR AN XML FILE VIA THE PATENT ELECTRONIC SYSTEM: The specification is required to include an incorporation-by-reference of electronic documents that are to become part of the permanent United States Patent and Trademark Office records in the file of a patent application. See 37 CFR 1.77(b)(5) and MPEP § 608.05. See also the Legal Framework for Patent Electronic System posted on the USPTO website (https://www.uspto.gov/sites/default/files/documents/2019LegalFrameworkPES.pdf) and MPEP § 502.05
(f) STATEMENT REGARDING PRIOR DISCLOSURES BY THE INVENTOR OR A JOINT INVENTOR. See 35 U.S.C. 102(b) and 37 CFR 1.77.
(g) BACKGROUND OF THE INVENTION: See MPEP § 608.01(c). The specification should set forth the Background of the Invention in two parts:
(1) Field of the Invention: A statement of the field of art to which the invention pertains. This statement may include a paraphrasing of the applicable U.S. patent classification definitions of the subject matter of the claimed invention. This item may also be titled “Technical Field.”
(2) Description of the Related Art including information disclosed under 37 CFR 1.97 and 37 CFR 1.98: A description of the related art known to the applicant and including, if applicable, references to specific related art and problems involved in the prior art which are solved by the applicant' s invention. This item may also be titled “Background Art.”
(h) BRIEF SUMMARY OF THE INVENTION: See MPEP § 608.01(d). A brief summary or general statement of the invention as set forth in 37 CFR 1.73. The summary is separate and distinct from the abstract and is directed toward the invention rather than the disclosure as a whole. The summary may point out the advantages of the invention or how it solves problems previously existent in the prior art (and preferably indicated in the Background of the Invention). In chemical cases it should point out in general terms the utility of the invention. If possible, the nature and gist of the invention or the inventive concept should be set forth. Objects of the invention should be treated briefly and only to the extent that they contribute to an understanding of the invention.
(i) BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING(S): See MPEP § 608.01(f). A reference to and brief description of the drawing(s) as set forth in 37 CFR 1.74.
(j) DETAILED DESCRIPTION OF THE INVENTION: See MPEP § 608.01(g). A description of the preferred embodiment(s) of the invention as required in 37 CFR 1.71. The description should be as short and specific as is necessary to describe the invention adequately and accurately. Where elements or groups of elements, compounds, and processes, which are conventional and generally widely known in the field of the invention described, and their exact nature or type is not necessary for an understanding and use of the invention by a person skilled in the art, they should not be described in detail. However, where particularly complicated subject matter is involved or where the elements, compounds, or processes may not be commonly or widely known in the field, the specification should refer to another patent or readily available publication which adequately describes the subject matter.
(k) CLAIM OR CLAIMS: See 37 CFR 1.75 and MPEP § 608.01(m). The claim or claims must commence on a separate sheet or electronic page (37 CFR 1.52(b)(3)). Where a claim sets forth a plurality of elements or steps, each element or step of the claim should be separated by a line indentation. There may be plural indentations to further segregate subcombinations or related steps. See 37 CFR 1.75 and MPEP 608.01(i) - (p).
(l) ABSTRACT OF THE DISCLOSURE: See 37 CFR 1.72 (b) and MPEP § 608.01(b). The abstract is a brief narrative of the disclosure as a whole, as concise as the disclosure permits, in a single paragraph preferably not exceeding 150 words, commencing on a separate sheet following the claims. In an international application which has entered the national stage (37 CFR 1.491(b)), the applicant need not submit an abstract commencing on a separate sheet if an abstract was published with the international application under PCT Article 21. The abstract that appears on the cover page of the pamphlet published by the International Bureau (IB) of the World Intellectual Property Organization (WIPO) is the abstract that will be used by the USPTO. See MPEP § 1893.03(e).
(m) SEQUENCE LISTING: See 37 CFR 1.821 - 1.825 and MPEP §§ 2421 - 2431. The requirement for a sequence listing applies to all sequences disclosed in a given application, whether the sequences are claimed or not. See MPEP § 2422.01.
The specification is also objected to because it contains what appears to be a large listing/table of data in the section entitled “Supporting Information” [starting on page 18] consisting of more than 90 pages “GEO datasets” in ASCII format. As such, the examiner cannot understand how to make use of or interpret this information for purposes of examination. As a result, the specification is objected to for lack of correspondence between the specification and claims as required by 37 CFR 1.75(d)(1), which states that the specification must provide the needed support or antecedent basis for the claim terms. See MPEP § 608.01(o) and MPEP § 2181, subsection IV. Applicant is required to make appropriate amendment to the description to provide clear support or antecedent basis for the claim terms provided no new matter is introduced, or amend the claims. See also MPEP 608.05(b) ASCII Plain Text Submissions of “Large Tables” and Treatment of Lengthy Tables in a Specification for Patents and Patent Application Publications. In accordance with 37 CFR 1.58(c)(1), applicant can file a paper version of the table in compliance with 37 CFR 1.52 or file a PDF version via the USPTO patent electronic filing system, and change all appropriate references to the former table in text format to the newly added paper or PDF version of the table in the remainder of the specification.
Claim Rejections - 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 5 and 7-9 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Claim 5 is drawn to a device that is “provided with a control unit” that performs a function (using a model “on an omics database”). However, the device as claimed does not explicitly comprise said “control unit” and a review of the specification does not define the claimed “control unit” such that it is necessarily interpreted to be an actual structural element of the device. Therefore the claimed device encompasses a program, per se, since the claimed “control unit” performs functions and is not explicitly required to have a physical structure. With regards to said “omics database”, it is not clear what functional relationship is intended between the database and “control unit” since it is well understood that a database merely stores data and does not perform any processing functions. Moreover, a database, even when carried on a physical medium, is nonfunctional descriptive material and is not statutory subject matter. As such, a combination of a database and a program, per se, does not render either statutory. For these reasons, the claimed device is not limited to comprise any hardware element or combination of software and hardware such that it is interpreted to be a physical article of manufacture. Accordingly, the device as claimed is not statutory subject matter. For an updated discussion of statutory considerations with regard to non-functional descriptive material and computer-related inventions see MPEP 2111.05 and MPEP 2106.
Claim Rejections - 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 5 and 7-8 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and ‘as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355).
Guidance: Step 1. Under the broadest reasonable interpretation, the claimed invention is directed to a device for performing a process and therefore falls within one of the four statutory categories.
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. In this case, the following steps of claim 1 recite an abstract idea:
wherein the control unit performs a topic analysis using a topic model on an omics database derived from two or more biofeatures linked to information indicating a disease name to estimate missing biofeatures for a particular disease, wherein the estimated missing biofeatures suggest the novel diagnostic biomarkers and/or therapeutic targets
Mental Processes
Under MPEP §2111, during patent examination, claims must be interpreted in their broadest reasonable manner consistent with the specification. This means that examiners consider the claim language in light of the specification as understood by a person of ordinary skill in the art, ensuring that the claims are not unduly narrowed by implicit limitations not explicitly recited in the claim (37 CFR 1.75(d)(1)).
In this case, the topic analysis is recited at a high level of generality and is not limited to any particular techniques or operations. Accordingly, under the BRI, these steps set forth or describe observing and/or analyzing data, which scientists can perform using their brains or a pencil and paper. As such, these steps encompass a mental process of observing data and/or manipulating data. MPEP 2106.04(a)(2), section III.
It is important to note that “Claims that recite performing information analysis as well as the collection and manipulation of information related to such analysis, have been determined by our reviewing court to be an abstract concept that is not patent eligible. See SAP, 898 F.3d, 1165, 1167, 1168 (Claims reciting "[a] method for providing statistical analysis" (id. at 1165) were determined to be "directed to an abstract idea" (id. at 1168)); see also Content Extraction & Transmission LLC v. Wells Fargo Bank, Nat'l Ass 'n, 776 F.3d 1343, 1345, 1347 (Fed. Cir. 2014). [Step 2A, Prong 1: YES].
Mathematical Concept
In addition, the claim requires performing topic analysis using a topic model. A review of the specification describes the topic model in terms of mathematical formula and parameters [see, e.g. ¶0024-25, and Figure 2]. Accordingly, under the BRI, this step sets forth or describes using mathematical algorithms and/or mathematically relating data. As such, this step encompasses a mathematical concept of manipulating information through mathematical correlations or calculations. MPEP 2106.04(a)(2) Section I. It is important to note that a mathematical concept need not be expressed in mathematical symbols, because “[w]ords used in a claim operating on data to solve a problem can serve the same purpose as a formula.” In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). [Step 2A, Prong 1: YES].
B. Guidance Step 2A, Prong 2
Having made that determination, under the 2019 Guidance, the examiner next determines whether there are additional elements beyond the recited abstract idea(s) that integrate them into a practical application.
In this case, the additional steps/elements that are not part of the abstract idea are as follows: a “control unit” and “database” (as recited in claim 5)
The additional elements directed to a control unit and database are generically recited and amount to nothing more than generic computer components being used as a tool to perform generic computer functions or the abstract idea. See MPEP 2106.05(b).
In summary, the claimed invention does not provide any objective evidence of an improvement to the technology, nor does the specification explain the details of an unconventional technical solution expressed in the claim, or identify technical improvements realized by the claim over the prior art. See MPEP 2106.04(d)(1) and MPEP 2106.05(a). Therefore, even when viewed in combination, these additional steps/elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO].
C. Guidance Step 2B:
This part of the eligibility analysis evaluates whether the claim as a whole amount to significantly more than the recited exception i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. See MPEP 2106.05.
As discussed above, the non-abstract steps/elements amount to nothing more than insignificant extra-solution activity. In addition, with regards to the claimed control unit and database, as discussed above, these are generically recited, routine and conventional elements, and the courts have explained that the use of generic computer elements do not alone transform an otherwise abstract idea into patent-eligible subject matter. See DDR Holdings (Fed. Cir. 2014). Therefore, even upon reconsideration, there is nothing unconventional with regards to the above non-abstract elements/steps. See MPEP 2106.05(d)(Part II). Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
Dependent Claims
Dependent claims 7-9 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. Regarding claim(s) 7-9, these claims are directed to limitations that further limit the specificity of the abstract idea set forth above or the nature of the data being used by the abstract idea. Accordingly, these steps also recite an abstract idea for reasons discussed above in the Step 2A (prong 1) analysis. Therefore, the claims as a whole are not patent eligible. For additional guidance, applicant is directed generally to MPEP 2106.
Claim Rejections - 35 USC § 112a
The following is a quotation of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same and shall set forth the best mode contemplated by the inventor of carrying out his invention.
The following is a written description rejection.
Claims 5 and 7-9 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The written description requirement is separate and distinct from the enablement requirement. The specification must: (1) describe the claimed invention in a manner understandable to a person of ordinary skill in the art, and (2) show that the inventor actually invented the claimed subject matter.
Regarding claim(s) 5, the specification fails to provide written description support for the following steps:
wherein the control unit performs a topic analysis using a topic model on an omics database derived from two or more biofeatures linked to information indicating a disease name to estimate missing biofeatures for a particular disease, wherein the estimated missing biofeatures suggest the novel diagnostic biomarkers and/or therapeutic targets
With regards to claimed function of performing “topic analysis using a topic model on an omics database”, this step is not limited to any particular acts or operations, any particular “biofeatures” or “estimated missing biofeatures”, any particular diagnostic biomarkers, or any particular therapeutic targets. A review of the specification fails to provide sufficient evidence that applicant had possession of the claimed “topic analysis”, models, and associated biofeatures for the full scope of what is being claimed. The specification does generally disclose a ‘generative model’ of proposed topic models along with specific equations [0024, 0025]. However, this is narrower in scope than what is claimed and it is improper to import narrowing limitations into the claims. MPEP 2111.01. Moreover, this disclosure does not provide any significant structural or functional details with regards to how the claimed model operates using the claimed data to achieve the claimed function, i.e. how it was derived, trained, and/or validated, or provide any correlations between biofeatures (or missing biofeatures) and novel biomarkers or therapeutic targets. In other words, the claimed model is essentially a black box to achieve the claimed function (estimate missing biofeatures). One of ordinary skill in the art would recognize that methods for developing models to estimate biofeatures for a particular disease are not trivial, and that models and biofeatures will vary depending upon the nature of the disease under investigation and the associated biomarkers or therapeutic targets.
This position is further supported by the prior art of Matsutani et al. (IDS filed 05/06/2025), which teaches methods for discovering novel mutation signatures. Unlike the claimed method, Matsutani is limited to specific disease (cancer), specific novel mutation signatures of the cancer genome, and a specific type of mathematical model and technique (latent Dirichlet allocation with variational Bayes inference). Matsutani performs cluster analyses for estimated mutation signatures to extract novel mutation signatures that appear in multiple primary lesions. Matsutani also teaches it is necessary to select a ‘representative’ signature from all the primary lesions in which that mutational process acts. See entire.
Das et al. (Scientific Reports, 2021, 11:24077, pp.1-16) teaches developing a statistical model (TiMEG) for the identification of disease-associated biomarkers in a case–control paradigm by integrating specific multi-omics data types, especially, in presence of missing omics data. Unlike the claimed device, the model incorporates the effect of genotype on methylation and also the effect of genotype, methylation, gene expression, and covariates on disease status. Das also applies the model using a specific tuberous sclerosis dataset to identify functionally relevant genes in the disease pathway. Das also notes that the presence of missing data poses a major challenge in data integration. See entire.
Harley et al. (WO2020/077352) teaches a method for utilizing multi-omic data indices for tumor profiling. In particular, Harley teaches the use of well-defined predictive models that require specific training and validation [see entire, e.g. 0049-0075, 0092] and that data integration and harmonization poses a particularly acute challenge in cancer sequencing, namely, standardization and integration to allow the user to incorporate multiple sources of data and identify clinically and biologically relevant information.
For these reasons, neither the instant claims nor the specification provides sufficient written description of these specific models (in terms of mathematical structure) such that one of skill in the art would have been aware that applicants were actually in possession of a device comprising a topic model configured to perform the full scope of what is presently claimed. “[A] sufficient description of a genus . . . requires the disclosure of either a representative number* of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can 'visualize or recognize' the members of the genus” (AbbVie, 759 F.3d at 1297, reiterating Eli Lilly, 119 F.3d at 1568-69)(emphasis added).
For the reasons discussed above, the specification does not satisfy the written description requirement with respect to the full scope of what is being claimed. For more information regarding the written description requirement, see MPEP §2161.01- §2163.07(b).
Claim rejections - 35 USC § 112b
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 5 and 7-9 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 pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 5 are also rejected due to said dependency.
Claim 5 recites “A device…provided with a control unit”. Firstly, it is unclear what is meant by the phrase “provided with” such that the artisan would know what structural and/or functional limitation is intended. Secondly, it is unclear as to the metes and bounds of the claimed “control unit” such that the artisan would know what structural limitation is intended. The specification does not provide any limiting definition for this term and does not correlate any specific structures with the claimed control unit. As such, it is unclear whether the claimed UNIT is a program, structural entity, or otherwise. The specification does disclose a diagram including a CPU, input device, and output device [Figure 3]. However, this does not amount to a limiting definition such that one of skill in the art would recognize what structural limitation is intended by said “control unit” and/or what specialized internal structure is intended. As a result, it is also unclear as to the metes and bounds of the claimed “device” such that the artisan would understand the scope of this term and what elements are minimalized comprised by the device as claimed. Clarification is requested via amendment. The examiner suggests, for example, amending claim 5 to include a computer processor, non-transitory computer readable medium, memory, and any other hardware elements required to practice the claimed invention (provided there is support for such elements in the specification).
Claim 5 recites “performs a topic analysis using a topic model on an omics database derived from two or more biofeatures linked to information indicating a disease name to estimate missing biofeatures for a particular disease”. This phrase is problematic for the following reasons. (1) It is unclear as to the metes and bounds of performing “topical analysis…to estimate missing biofeatures for a particular disease”. The claim is not limited to any particular acts, model, or “missing biofeatures” data and without reciting the particular structure, materials or steps that accomplish the function or achieve the result, the claim fails “to provide a clear-cut indication of the scope of the subject matter embraced by the claim”. See MPEP 2173.05(g). As a result, it is unclear what computational techniques are included or excluded by the claimed “topic analysis” such that one of ordinary skill in the art would know how to avoid infringement, i.e. in what way does the generically recited “topic analysis” result in estimating “missing biofeatures”. Clarification is requested via amendment.
(2) It is unclear as to the metes and bounds of “missing biofeatures”, which amounts to a negative limitation. Negative limitations are permitted if they clearly define claim boundaries. MPEP §2173.05(i). In this case, however, neither the claim nor the specification provides any limiting definition for the term “missing biofeatures” (or biofeatures) that would serve to clarify the scope of this term. Clarification is requested via amendment.
(3) With regard to “using a topic model”, it is unclear as to the metes and bounds of this term such that the artisan would know what structural limitation is intended. A review of the specification does not provide any limiting definitions that would serve to clarify the scope of this term such that the artisan would know how to avoid infringement, i.e. what structural elements of the claimed model are intended. The specification does provide a limited example of a topic model in terms of mathematical formula and parameters [see, e.g. ¶0024-25, and Figure 2]. However, examples are not limiting definitions and it is improper to import narrowing limitations into the claims. MPEP 2111.01. As a result, it is also unclear in what way the claimed model is being used to achieve the intended function. The claim does not provide any relationship between the model and the “missing biofeatures” and a claim is indefinite where it merely recites a use without any active, positive steps delimiting how this use is actually practiced. See MPEP § 2173.05(q). Clarification is requested via amendment.
(4) It is unclear as to the metes and bounds of the term “omics database” such that the artisan would know how to avoid infringement, i.e. what type of data is necessarily included or excluded that would serve to differentiate from any other database. A review of the specification does not provide any limiting definition that would serve to clarify the scope. In addition, it is unclear if this database is intended to be a structural element of the claimed device or otherwise. Clarification is requested via amendment.
(5) With regards to the phrase “derived from two or more biofeatures linked to information indicating a disease name to estimate missing biofeatures for a particular disease”, this is a product-by-process type limitation directed to how the model was “derived” at some previous point in time. As a result, it is also unclear in what way biofeatures are being used to “derive” the claimed database and what limiting effect of the claimed device is intended. See also MPEP § 2111.04. Clarification is requested via amendment.
Claim 5 recites “wherein the estimated missing biofeatures suggest the novel diagnostic biomarkers and/or therapeutic targets.” It is unclear what limiting effect is intended by the above “wherein” clause, i.e. what are the metes and bounds of the estimated missing biofeatures and in what way do they suggest a novel diagnostic biomarker and/or therapeutic targets. A review of the specification does not provide any limiting definition that would serve to clarify the scope. Applicant is reminded that claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed. See MPEP 2111.04. Clarification is requested via amendment.
Claim 8 recites “wherein the topic model is based on Latent Dirichlet Allocation model”. It is unclear in what way the claimed topic model is “based on” Latent Dirichlet Allocation model. A review of the specification does not provide any limiting definitions that would serve to clarify the scope of this term such that the artisan would know how to avoid infringement, i.e. what structural elements of the claimed model are intended. The specification does provide a limited example of a topic model in terms of mathematical formula and parameters [see, e.g. ¶0024-25, and Figure 2], as discussed above. However, examples are not limiting definitions and it is improper to import narrowing limitations into the claims. MPEP 2111.01. Clarification is requested via amendment. In addition, the phrase “based on Latent Dirichlet Allocation model” appears to be grammatically incorrect and should recite “based on a Latent Dirichlet Allocation model”.
Claim 9 recites “wherein the control unit verifies the reliability of the extracted missing biofeatures”. Firstly, the term “reliability” is a relative term and specification does not provide any limiting definitions, specific properties, or criteria that would serve to clarify the scope, i.e. the result is subjective and imperceptible. Moreover, the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement. Clarification is requested via amendment. Secondly, it is unclear what is meant by “extracted missing biofeatures”. Parent claim 5 does recite an intended use “to estimate missing biofeatures” but this is not the same as “extracted missing biofeatures”. As such, it is unclear what “extracted missing biofeatures” is referring to. Clarification is requested via amendment. Secondly, with regards to the “wherein” clause,
Claim Interpretation - 35 USC § 112f
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier.
Regarding claim(s) 5, such claim limitation(s) is/are: “control unit.” Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Citation of Relevant Prior Art
In view of the indefiniteness and lack of clarity in the instant claims, as set forth in the 35 USC 112(b) rejections above, the Examiner has had difficulty in properly interpreting instant claims. However, to avoid piecemeal prosecution and to give applicant a better appreciation for relevant prior art if the claims are redrafted to avoid the 35 USC 112(b) rejections, the following prior art made of record and not relied upon is considered pertinent to applicant' s disclosure.
Subramanian et al. (Bioinformatics and Biology Insights, 2020, Volume 14: 1–24) teaches a review of several different tools and methods developed for data integration and interpretation and analyzing multiple omics data to address applications such as disease subtyping, biomarker prediction, and deriving insights into the data. They provide the methodology, use-cases, and limitations of these tools; brief account of multi-omics data repositories and visualization portals; and challenges associated with multi-omics data integration.
Harley et al. (WO2020/077352), which teaches a method for utilizing multi-omic data indices for tumor profiling. The method can comprise storing a plurality of multi-omic data indices; ingesting additional multi-omic data and any annotations associated with the additional multi-omic data; indexing the ingested additional multi-omic data and annotations to produce tokenized ingested additional multi-omic data; receiving a user query; selecting one or more relevant multi-omic data indices based on the user query; ranking the selected one or more multi-omic data indices based on at least one of clinical actionability, pathogenicity, feature weight, or frequency; and returning the ranked one or more multi-omic data indices to the user. Harley teaches that data integration and harmonization poses a particularly acute challenge in cancer sequencing, namely, standardization and integration to allow the user to incorporate multiple sources of data and identify clinically and biologically relevant information.
Das et al. (Scientific Reports, 2021, 11:24077, pp.1-16) teaches developing a statistical model (TiMEG) for the identification of disease-associated biomarkers in a case–control paradigm by integrating specific multi-omics data types, especially, in presence of missing omics data. Unlike the claimed device, the model incorporates the effect of genotype on methylation and also the effect of genotype, methylation, gene expression, and covariates on disease status. Das also applies the model using a specific tuberous sclerosis dataset to identify functionally relevant genes in the disease pathway. Das also notes that the presence of missing data poses a major challenge in data integration. See entire.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619
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