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 .
Status of the Claims
The claim set received 25 August 2025 has been entered into the application.
Claims 43-47 are new.
Claims 1-22 are previously cancelled.
Claims 40-42 are cancelled.
Claim(s) 23-39 and 43-47 are pending.
Priority
Acknowledgment is made of applicant’s claim to priority to U.S. Provisional Application No. 62/016,078 filed on 27 April 2020.
Drawings
The objection to the drawings in the Office Action mailed 28 January 2025 is withdrawn in view of the replacement drawings filed 28 July 2025 and 25 August 2025.
The drawings were received on 28 July 2025 and 25 August 2025. These drawings are accepted.
Specification
The amendments to the specification regarding the replacement drawing sheet received 25 August 2025 have been entered into the application.
The objection to the specification because unique uncorrected joint p-value of claim 33 in the Office Action mailed 28 January 2025 is withdrawn in view amendments received 25 August 2025.
The amendment filed 22 December 2023 and 25 August 2025 are objected to under 35 U.S.C. 132(a) because it introduces new matter into the disclosure. 35 U.S.C. 132(a) states that no amendment shall introduce new matter into the disclosure of the invention. The added material which is not supported by the original disclosure is as follows:
The added material not supported is “member” of claims 23, 27-31, 33, and 37-39. (filed 22 December 2023).
The added material not support is “pathway-specific unique uncorrected joint p-value unique” of claim 33. (filed 25 August 2025).
Applicant is required to cancel the new matter in the reply to this Office Action.
Response to Arguments
Applicant’s arguments filed 25 August 2025, have been fully considered but the objection is maintained.
It is noted that the Applicant was not responsive with respect to canceling the new matter from the claims. Therefore, the objection to the specification is maintained. It is noted that amending uncorrected joint p-value to recite unique pathway specific uncorrected joint p-value does not obviate the objection because the specification only supports combining the first and second probabilities and does not support a “pathway specific uncorrected joint p-value” as described in the 35 U.S.C § 112(a) new matter rejection below.
Claim Rejections - 35 USC § 112
35 U.S.C § 112(a)
The instant rejection is maintained for reason for record in the Office Action mailed 28 January 2025 and modified in view of the amendments filed 25 August 2025.
The rejection of claim 40-42 under 35 U.S.C § 112(a) in the Office Action mailed 28 January 2025 is withdrawn in view amendments received 25 August 2025.
The rejection of claim 33 “unique uncorrected joint p-value” under 35 U.S.C § 112(a) in the Office Action mailed 28 January 2025 is withdrawn in view amendments received 25 August 2025.
The following is a quotation of the first paragraph 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 the first paragraph of pre-AIA 35 U.S.C. 112:
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.
Claims 23-39 and 43-46 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
This is a New Matter rejection based on the new introduced claims filed 22 December 2023 and 25 August 2025. With respect to the new matter introduced on 22 December 2023, the Applicant has not cancelled or amended the new matter from the claims.
Claims 23, 28, and 37 require identifying a member by selecting the member from a group consisting of a biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator perturbed by the set of biomolecules affected by the phenotype. The limitation “member” is required to determine the targeted drug treatment and determining probabilities which is further used for treating the subject with a targeted drug treatment and/or administering the targeted drug treatment. However, the specification does not encompass literal or figurative support for limitation “member”. In addition, the original claim set received 27 April 2021 does not appear contain the limitation “member”. The due to lack of written description for identifying a “member,” the specification also does not provide guidance as to how the “member” is utilized to determine the targeted treatment configured to reverse expression of the set of biomolecules. The claims appear to depend on the data of the member to identify a targeted drug treatment and to treat a subject with the identified targeted drug treatment, but do not provide guidance as to what data of the “member” is utilized and incorporated in the claims. The amended limitation “member” is new matter.
With respect to claims 28, 33 and 37, the claim utilizes the limitation “unique pathway-specific uncorrected joint p-value”. The specification does not provide literal or figurative support and guidance as to what encompasses “unique pathway-specific uncorrected joint p-value” or “unique pathway-specific uncorrected joint p-value for multiple comparisons”. The specification provides guidance for using a “a unique pathway-specific uncorrected combined p-value”, but does not provide guidance for using “a unique pathway-specific uncorrected joint p-value”. The amended limitation “unique pathway-specific uncorrected joint p-value” is new matter.
It is recommended that the applicant amend the claims to recite unique pathway-specific uncorrected “combined” p-value to provide language consist with the specification. It is further recommended to amend the claims 23, 33, and 37 identifying a member step to recite “identifying a biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator, wherein the biological pathway, the biological mechanism, the biological process, the biochemical function, and the upstream regulator are selected from a group consisting of biological pathways, biological mechanisms, biological processes, biochemical functions, and upstream regulators perturbed by the set of biomolecules affected by the phenotype” to provide clarity and language and limitations consistent with the specification.
Claims 24-36, 38-39, and 43-46 are rejected because the base claims from which they depend are rejected and the claims fail to provide limitation to overcome the deficiencies of the base claims.
All new matter is required to be cancelled or amended in the reply to this action.
Response to Arguments
Applicant’s arguments filed 25 August 2025, have been fully considered but the rejection is maintained. However, upon further consideration, a new ground(s) of rejection is made in view of the amendments filed 25 August 2025.
It is noted that the Applicant did not cancel or amend the new matter “member” from the claims as required above.
The Applicant states “The rejection under 35 U.S.C. § l 12(a) alleging that the term "member" lacks written description support is misplaced. The term "member" does not introduce new matter, nor does it require explicit support in the specification. In the context of the claims, "member" is simply a generic linguistic term used to refer to individual parts of a list (e.g., a "Markush group"), which is a common and accepted usage in U.S. patent law. It does not represent a separate or novel concept that demands specific written description support.” [remarks, page 12]. The Applicant states “Furthermore, the disputed portion of the claim is structured as a conventional Markush group, which inherently defines a closed set of alternatives. The claim explicitly recites the Markush group as consisting of: (1) a biological pathway, (2) a biological mechanism, (3) a biological process, (4) a biochemical function, and (5) an upstream regulator perturbed by the set of biomolecules affected by the phenotype. By definition, the individual parts of the Markush group are the "members" of the group. Therefore, the term "member" is nothing more than a shorthand reference to an individual element of the Markush group, which does not require separate or explicit written description support in the specification. A person of ordinary skill in the art would immediately understand that the term "member" refers to any one of the enumerated elements of the group. The specification provides written support for the individual parts of the group, including biological pathways, mechanisms, processes, functions, and regulators. As such, the Markush group structure inherently provides support for the term "member," making the rejection unwarranted. With respect to connecting up the claimed group members with the specification as originally filed, and based upon the advanced knowledge of one skilled in the life sciences and bioinformatics, Applicant respectfully submits that the members of the grouping of Claim 23 ("a member selected from the group consisting of a biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator") are supported by reference to the specification as follows, taking each group member in turn.” [remarks, page 13-14]. The Applicant points to the specification paragraphs [0017, 0055, 0076, 0016, 0049, 0060, 0079-0080, 0083, 0037, 0052-0053, 0035-0036] for guidance with respect to the term “member” [remarks, pages 13-14].
In response, the term “member” is considered an integral part of the selection of the group. Here, the member, under Broadest Reasonable Interpretation (BRI), can be interpreted as any member or sub-section of a pathway (which pathway), mechanism (which mechanism), biological process (which biological process), a biochemical function (which biochemical function), and an upstream regulator (which gene) is perturbed by a set of molecules. Although the member is selected from a group, the member is new matter because it does not define or specify what the member of the group consisting of a biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator perturbed by the set of biomolecules affected by the phenotype is used for determining a targeted drug treatment that is subsequently administered. As such, “member” is new matter because the specification does not provide a definition for what is to encompass the member from each member of the Markush group. Although the limitations are part of a Markush group, it doesn’t preclude the limitation from containing new matter as the “member” is not defined or specified in such way that one of ordinary skill in the art would recognize as to what member from the pathways, processes, mechanisms, biological functions, or upstream regulators are being identified to which a targeted treatment can be determined and administered. Therefore, support for the ”member” is required because one of ordinary skill in the art would not be able to treat a patient with a targeted treatment based on any member (i.e., process, function, pathway, gene) in order to treat a patient with coronavirus. It is noted that the claim language is written such that a “member” can encompass any pathway from biological pathway, any mechanism from a biological mechanism, any process from biological processes, any function from a biochemical function, and any upstream regulator (i.e., gene, poly A tail, stop codon), for example.
It is noted that on pages 13-14 of the remarks that the Applicant has provided support from the specification regarding the group of claims 23 and 37 but the Applicant did not point out what specific data is used for selecting a member. The Applicant does not provide support for the limitation “member”. For example, claim 23 recites identifying a member selected from a group consisting of a biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator perturbed by the set of biomolecules affected by the phenotype, but the specification, claims and arguments do not provide as to what data or attributes the member is to comprise from the groups for determining a target treatment for treatment of a phenotype associated with a corona virus. The argument is not persuasive because, in view of the specification and the claims, there is no support for the limitation “member” encompassing a data selected from a group consisting of a biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator perturbed by the set of biomolecules affected by the phenotype. It is recommended to amend the claims as noted in the 35 U.S.C § 112(a) above. The argument is not further persuasive because the Applicant has not provided what data is utilized for limiting the limitation “member” and what data is utilized for identifying the member for administering a targeted drug treatment. Therefore, the rejection regarding “identifying a “member” selected” is maintained because the Applicant has not cancelled or amended the limitation to provide clarity with respect to what data or other attributes the “member” is to comprise.
The Applicant states “that the rejection under 35 U.S.C. § l 12(a) alleging that the limitation "unique uncorrected joint p-value" lacks written description support is improper. The specification provides support for this limitation in paragraph 14, which states: In one aspect, the method further includes combining the first probability value (pORA) and the second probability value (pACC) so as to determine a unique pathway-specific uncorrected p-value for each of the one or more biological pathways.” [remarks, page 14]. The Applicant points to specification Paragraph 14 describes how the first and second probability values are combined to create a "unique pathway-specific uncorrected p-value." The addition of the word "joint" in the claims is merely for clarity purposes, as it accurately reflects the combination of the two probability values into a single p-value. A person of ordinary skill in the art would readily understand that the term "joint" in this context refers to the p-value resulting from the combination of the two distinct probabilities. To further clarify the claim language” The Applicant states claims have been amended such that each instance of "unique uncorrected joint p-value" to read "pathway-specific unique uncorrected joint p-value." This amendment aligns the claim language with the terminology used in the specification.” [remarks, page 14].
In response, the argument is not persuasive because the "pathway-specific unique uncorrected joint p-value” is not supported by the specification. Here, it is acknowledged that the Applicant may be their own lexicographer. It is noted that an applicant is entitled to be their own lexicographer and may rebut the presumption that claim terms are to be given their ordinary and customary meaning by clearly setting forth a definition of the term that is different from its ordinary and customary meaning(s) in the specification at the relevant time. However, it is important to note that any special meaning assigned to a term “must be sufficiently clear in the specification that any departure from common usage would be so understood by a person of experience in the field of the invention.” Multiform Desiccants Inc. v. Medzam Ltd., 133 F.3d 1473, 1477, 45 USPQ2d 1429, 1432 (Fed. Cir. 1998). See MPEP 2111.01 (IV)(A). Here, providing a joint probability is not supported in the specification because as noted by the Applicant [remarks, page 14], the term “joint” is used to clarify the combined first and second values. Here, the specification discloses “the method further includes combining the first probability value (pORA) and the second probability value (pACC) so as to determine a unique pathway-specific uncorrected p-value for each of the one or more biological pathways.”. The term “joint” with respect to encompassing a “pathway-specific unique uncorrected joint p-value” is not disclosed throughout the specification such that it describes a statistical joint probability “pathway-specific unique uncorrected joint p-value” sufficiently clear so that one of ordinary skill in the art can mathematical differentiate between the formula for calcualting “pathway-specific unique uncorrected joint p-value” compared to combining probability values to determine a targeted treatment. However, combining the results of first probability value (pORA) and the second probability value (pACC) so as to determine a unique pathway-specific uncorrected p-value is not the same as a mathematical/statistical formula “pathway-specific unique uncorrected joint p-value” which suggests the “pathway-specific unique uncorrected joint p-value” is a specific formula for calculating a “pathway-specific unique uncorrected joint p-value”, not merely combining data (i.e., combining the first probability value (pORA) and the second probability value (pACC)) to determine a result “pathway-specific unique uncorrected joint p-value”. Furthermore, it is known in the art that “joint” and “combine” entail different meanings in the art of statistics with respect to probabilities. For example, “joint probability" is a specific term for the probability of two or more events occurring simultaneously, while "combined" is a more general term that can refer to combining probabilities in different ways, such as with "or" (union) or "and" (intersection). The key distinction is that "joint" probability specifically refers to the intersection of events ("and"), not their union ("or"). Therefore, the argument is not persuasive, and it is recommended to amend the claims as recommended by the Examiner to obviate the rejection.
35 U.S.C § 112(b)
The instant rejection is maintained for reason for record in the Office Action mailed 28 January 2025 and modified in view of the amendments filed 25 August 2025.
The rejection of claim 40-42 under 35 U.S.C § 112(a) in the Office Action mailed 28 January 2025 is withdrawn in view amendments received 25 August 2025.
The rejection of claim 33 under 35 U.S.C § 112(a) in the Office Action mailed 28 January 2025 is withdrawn in view amendments received 25 August 2025.
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 23-39 and 43-46 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
With respect to claims 23, 33, and 37, the metes and bounds of the limitation “member” is indefinite because the specification nor the claims provide a limiting definition for the term. One of ordinary skill in the art would not be apprised to know what the “member” is and what data encompasses the “member”. It is further indefinite because it is unclear if the member is a member from the group consisting biological pathway (chemokine signaling pathway), a biological mechanism (methylprednisolone mechanism of action), a biological process, a biochemical function, and an upstream regulator (a specific gene) or if the member is the biological pathway or a biological mechanism or a biological process or a biochemical function, or an upstream regulator, for example. One of ordinary skill in the art would not be apprised to know if the “member” is a gene, protein, or other molecule to which will be utilized to determine the targeted drug treatment and determine the pORA and pACC. It is further unclear what data of the “member” is used to determine the targeted drug treatment and determine the pORA and pACC. Here, the metes and bounds of the term “member” render the claims indefinite because it is not clear if the “member” is an entire biological pathway, biological mechanism, biological process, biochemical function, or upstream regulator or if the member is a sub section of a pathway (i.e., chemokine signaling pathway [Spec 0017]), mechanism (i.e., mechanism through which methylprednisolone act [Spec 0016] which mechanism), process (does not claim a specific process), function (i.e., metabolomics or catalysis [0049 and 0052]), or regulator (i.e., downstream gene and the arrow with the negative sign) which does not claim an upstream regulator. It is recommended to amend the claims to clarify if the member is one of the five members of the group such as biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator or if the member is a subgroup or category of biological pathway (i.e., chemokine signaling pathway), a biological mechanism (i.e., methylprednisolone mechanism of action), a biological process, a biochemical function, and an upstream regulator (e.g., a specific gene) that is affected by a perturbation.
Claims 24-36, 38-39, and 43-46 are rejected because the base claims from which they depend fail to provide limitations to overcome the deficiencies of the base claims.
Response to Arguments
Applicant’s arguments filed 25 August 2025, have been fully considered and the rejection has been maintained. However, upon further consideration, a new ground(s) of rejection is made in view of the amendments filed 25 August 2025.
The Applicant states “claims 23 and 37 were amended to clarify that the "member" is one of the five members of the group consisting of (1) a biological pathway, (2) a biological mechanism, (3) a biological process, (4) a biochemical function, and (5) an upstream regulator perturbed by the set of biomolecules affected by the phenotype.” [remarks, page 15].
With respect to the rejection under 112(b), the Applicant did not address the limitation “member”. Therefore, the rejection regarding “member” is maintained.
Claim Rejections - 35 USC § 101
The instant rejection is maintained for reason for record in the Office Action mailed 28 January 2025 and modified in view of the amendments filed 25 August 2025. It is noted the amendments received 25 August 2025 are necessitated by new ground(s) of rejection.
The rejection of claim 40-42 under 35 U.S.C § 101 in the Office Action mailed 28 January 2025 is withdrawn in view amendments received 25 August 2025.
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 23-39 and 43-46 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Following the flowchart from MPEP 2106.
Step I - Process, Machine, Manufacture or Composition
Claims 23-39 and 43-46 are directed towards a method, so a process.
Claim 47 is drawn to method of treatment, so a process. However, the claim is drawn to statutory matter and is therefore not rejected.
2A Prong I - Identification of an Abstract Idea
Claim 23 recites:
Comparing a plurality of sets of biomolecules from the phenotype to a plurality of sets of biomolecules from a control.
This step can be performed in the human mind by observing and judging biomolecules of a phenotype and a control and is therefore an abstract idea.
Identifying a set of biomolecules of the sets of biomolecules from the phenotype that is affected by the phenotype, each biomolecule having a differential expression between the phenotype and the control.
This step can be performed in the human mind by observing and evaluating differential expression data between a set of biomolecules and controls and is therefore an abstract idea.
Identifying a member, wherein the member is selected from a group consisting of a biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator perturbed by the set of biomolecules affected by the phenotype.
This step can be performed in the human mind by observing and evaluating a perturbation to identify a member and is therefore an abstract idea.
Determining the targeted drug treatment configured to reverse the differential expression of the set of biomolecules based upon the member selected from the group consisting of the biological pathway, the biological mechanism, the biological process, the biochemical function, and the upstream regulator.
This step can be performed in the human by observing and evaluating data based on the selected member and is therefore an abstract idea.
Claim 37 recite:
Identifying a set of biomolecules affected by the phenotype, each biomolecule having a differential expression between the phenotype and a control.
This step can be performed in the human mind by observing and evaluating a set of biomolecules and a control and is therefore an abstract idea.
Identifying a member wherein the member is selected from a group consisting of a biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator perturbed by the set of biomolecules affected by the phenotype.
This step can be performed in the human mind by observing and evaluating a perturbed biological pathway, a biological mechanism, a biological process, a biochemical function, and an upstream regulator to select a member to identify and is therefore an abstract idea.
Determining a first probability including a first probability value of p over representation (pORA) representing a probability of observing an actual number of biomolecules affected by the phenotype in the member selected from the group consisting of the biological pathway, the biological mechanism, the biological process, the biochemical function, and the upstream regulator perturbed by the set of biomolecules affected by the phenotype just by chance.
This step can be performed in the human mind by following instructions to determine first probability value of p over representation (pORA) representing an observed number of biomolecules perturbed by the phenotype and is therefore an abstract idea. The step encompasses determining a value of p over representation (pORA) representing a probability of observing an actual number of biomolecules affected by the phenotype in the member selected from the group which encompasses performing mathematical/statistical computations to determine a probability and is therefore a further abstract idea.
Determining a second probability including a second probability value (pACC) representing the probability of observing a measured total perturbation accumulation in the member selected from the group consisting of the biological pathway, the biological mechanism, the biological process, the biochemical function, and the upstream regulator perturbed by the set of biomolecules affected by the phenotype just by chance.
This step can be performed in the human mind by following instructions to determine a second probability and is therefore an abstract idea. This step encompasses determining a second probability value (pACC) representing the probability of observing a measured total perturbation accumulation in the member selected which encompasses performing mathematical/statistical computations to determine a probability and is therefore a further abstract idea.
Combining the first probability value (pORA) and the second probability value (pACC) so as to determine a unique pathway specific uncorrected joint p-value for the member selected from the group consisting of the biological pathway, the biological mechanism, the biological process, the biochemical function, and the upstream regulator perturbed by the set of biomolecules affected by the phenotype just by chance.
This step can be performed in the human mind by organizing and combining data from the pORA and the pACC to determine an unique pathway specific uncorrected joint p-value for the member selected from the group and is therefore an abstract idea. The step encompasses combining the data of the pORA and pACC to determine an unique pathway-specific uncorrected joint p-value for the member which encompasses performing mathematical/statistical computations to determine a probability and is therefore a further abstract idea.
Correcting the unique pathway-specific uncorrected joint p-value for multiple comparisons based on a number of members selected from the group consisting of the biological pathway, the biological mechanism, the biological process, the biochemical function, and the upstream regulator perturbed by the set of biomolecules affected by the phenotype using a False Discovery Rate (FDR) or Bonferroni correction method.
This step can be performed in the human mind following instructions to correct the uncorrected joint p-value for multiple comparisons based on a number of members selected from the group using a False Discovery Rate (FDR) or Bonferroni correction method and is therefore an abstract idea. The step encompasses correcting the uncorrected joint p-value using statistical operations such as using a False Discovery Rate (FDR) or Bonferroni correction method to correct data which encompasses performing mathematical/statistical computations to determine a probability and is therefore a further abstract idea.
Determining the targeted drug treatment configured to reverse the differential expression of the biomolecule based upon the member selected from the group consisting of the biological pathway, the biological mechanism, the biological process, the biochemical function, and the upstream regulator and selecting the targeted drug treatment when the corrected joint p-value is less than predetermined threshold and reverses the differential expression of two of the biomolecules.
This step can be performed in the human mind by observing, comparing, and evaluating a targeted drug treatment based on the member selected from a group and is therefore an abstract idea. This step can be performed in the human mind by observing and comparing the corrected joint p-value to select a targeted drug treatment and is therefore a further abstract idea.
Claims 24-25, 26-31, 33, 35-36, and 38-39 are further drawn to limitations that describe the abstract ideas of claims 23 and 37 and are therefore also abstract ideas.
2A Prong II - Consideration of Practical Application
Claims 23
Claim 23 does not recite any additional elements to which integrate the recited judicial exception into a practical application because administering of the targeted drug treatment (i.e., targeted drug treatment includes a composition comprising a compound selected from the group consisting of prednisolone, dexamethasone, diclofenac, myochrysine, esters thereof, derivatives thereof, salts thereof, and combinations thereof) is not integrated with the judicial exception. For example, claim 23 recites comparing biomolecules of the phenotype to a control set of biomolecules, identifying a set of biomolecules, identifying a member from a group of biological pathways, biological processes, biochemical functions, and upstream regulator perturbed by the set of biomolecules, determining a targeted drug treatment configured to reverse differential expression of the set of biomolecules based on the member selected from a group, and administering the targeted drug treatment. With respect to the particular treatment(s), the treatments are not integrated into a practical application because the treatments do not have more than a nominal or insignificant relationship to the exception(s). For example, the is a disconnect between the treatments and what is being treated. Here, claim 23 recites a subject having corona virus, but the claimed steps do not connect and/or provide a correlation between set of biomolecules to a biological pathway, biological processes, biological mechanism, biochemical functions, and an upstream regulator and the targeted treatments with respect to a corona virus infection. To exemplify, it is known in the art that diclofenac, dexamethasone, and prednisolone [Wiles, disclosure 0800] are utilized as anti-inflammatories. Esters are used for their anti-inflammatory properties [disclosure 0829-0830] while myochrysine is utilized in the art for treating rheumatoid arthritis (RA) [Wiles, disclosure 0813]. However, the claims do not correlate any sets of biomolecules and identified members to a determined targeted drug treatment in order to treat phenotypes induced by corona virus infection. Furthermore, there is not a significant or more than nominal relationship between a set of biomolecules and the treatment step. For example, the set of biomolecules can be any biomolecules, the member can be any biological pathway, process, or mechanism, any biochemical function, and any upstream regulator that can be treated using said targeted drug treatments. Thus, in context of claim 23, the administration step is not significantly related to the recited correlation of set of biomolecules and the members to the targeted drug treatments to reverse differential gene expression. As described by the MPEP 2106.04(d)(2)(a), that in order to qualify as a "treatment" or "prophylaxis" limitation for purposes of this consideration, the claim limitation in question must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. Here, the treatments are not particular as to treating a particular disease and the phenotype (i.e., treating a pathway from a corona virus infection that induces inflammation (i.e., cytokine-cytokine pathway or chemokine pathway)) to affect a type of change in a biological pathway, process, mechanism, biochemical function, and/or an upstream regulator such that the targeted drug treatment agonizes or antagonizes reverse differential gene expression. Although claim 23 recites a subject with corona virus, there is no natural law correlation between subject’s physiological response (i.e., set of biomolecules, members) perturbed by a corona virus and which differentially expressed genes are to be reversed. Claim 23 and the dependent claims do not connect which differentially expressed genes are reversed by using the target drug treatment. For example, claim 23 recites a member can be an upstream regulator(s), but the claims do not connect/correlate differential gene expression of any particular gene regulator(s) such that the gene (i.e., upstream regulator) regulation is reversed (i.e., affected) using the targeted drug treatments.
Alternatively, since it is known that diclofenac, dexamethasone, and prednisolone [Wiles, disclosure 0800] are utilized as anti-inflammatories, esters are used for their anti-inflammatory properties [disclosure 0829-0830] while myochrysine is utilized in the art for treating rheumatoid arthritis (RA) [Wiles, disclosure 0813], there is no correlation of treating the symptoms (i.e., inflammation from fevers, headaches, fatigue (i.e., phenotype)) of corona virus with the treatments in order to reverse differential expression of genes related to the phenotypes (i.e., symptoms of infection).
Therefore, the administration of the targeted drug treatments and the targeted drug treatments of claims 23 and 43-44 do not integrate the recited judicial exception into a practical application because the claims do not recite limitations that have more than a nominal or insignificant relationship to the exception(s). See MPEP 2106.04(d)(2)(b).
Claim 37
Claim 37 recites identifying a set of biomolecules. Claim 37 recite identifying a member selected from a group. Claim 37 recites determining a targeted drug treatment. Claim 37 recites determining a first probability (pORA) and a second probability (pACC). Claim 37 recites combining the pORA and the pACC to determine an uncorrected joint p-value for the selected member. Claims 37 recites correcting the uncorrected joint p-value. Claim 37 recites determining the targeted drug treatment when the corrected joint p-value is less than a threshold. Claims 37 recites administering the targeted treatments (i.e., targeted drug treatment includes a composition comprising a compound selected from the group consisting of prednisolone, dexamethasone, diclofenac, myochrysine, esters thereof, derivatives thereof, salts thereof, and combinations thereof) while claims 45-46 recite dosages and schedules for the administration of the myochrysine and diclofenac.
Claims 37 and 45-46 do not recite any additional elements to which integrate the recited judicial exception into a practical application because administering of the targeted drug treatment (i.e., targeted drug treatment includes a composition comprising a compound selected from the group consisting of prednisolone, dexamethasone, diclofenac, myochrysine, esters thereof, derivatives thereof, salts thereof, and combinations thereof) is not integrated with the judicial exception. For example, claim 37 recites comparing biomolecules of the phenotype to a control set of biomolecules, identifying a set of biomolecules, identifying a member from a group of biological pathways, biological processes, biochemical functions, and upstream regulator perturbed by the set of biomolecules, determining a first probability (pORA) and a second probability (pACC), combining the pORA and the pACC to determine an uncorrected joint p-value for the selected member, correcting the uncorrected joint p-value, determining the targeted drug treatment when the corrected joint p-value is less than a threshold, and administering the targeted drug treatment, but the treatments are not integrated into a practical application because the treatments do not have more than a nominal or insignificant relationship to the exception(s). For example, there is a disconnect and/or no correlation between the treatments and what is being treated. Here, claim 37 recites a subject having corona virus, but the claimed step does not connect and/or provide a correlation between set of biomolecules of a biological pathway, biological processes, biological mechanism, biochemical functions, and an upstream regulator and the targeted treatments. To exemplify, it is known in the art that diclofenac, dexamethasone, and prednisolone [Wiles, disclosure 0800] are utilized as anti-inflammatories. Esters are used for their anti-inflammatory properties [disclosure 0829-0830] while myochrysine is utilized in the art for treating rheumatoid arthritis (RA) [Wiles, disclosure 0813]. However, the claims do not correlate any sets of biomolecules and identified members (i.e., pathway, processes, mechanism, biochemical function, and upstream regulator) to a determined targeted drug treatment in order to treat symptoms induced by corona virus infection, such as inflammation. Furthermore, there is not a significant or more than nominal relationship between a set of biomolecules and the treatment step. For example, the set of biomolecules can be any biomolecules, the member can be any biological pathway, process, or mechanism, any biochemical function, and any upstream regulator that can be treated using said targeted drug treatments. Thus, in context of claim 37, the administration step is not significantly related to the recited correlation of set of biomolecules and the members to the targeted drug treatments to reverse differential gene expression. Additionally, there is a further disconnection between a subject infected with corona virus and the targeted treatments. For example, as described by the MPEP 2106.04(d)(2)(a), that in order to qualify as a "treatment" or "prophylaxis" limitation for purposes of this consideration, the claim limitation in question must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. Here, the treatments are not particular as to treating a particular disease and inducing a change in phenotype. Although claim 37 recites a subject with corona virus, there is no natural law correlation between subject’s physiological response (i.e., set of biomolecules, members) perturbed by a corona virus and between reversing differentially expressed genes using the target treatments to effect or change the disease or condition (i.e., phenotypes induced by a corona virus). Claim 37 and it associated dependent claims do not connect/correlate which differentially expressed genes are reversed using the target drug treatment. For example, claim 37 recites a member can be an upstream regulator(s), but the claims do not connect any particular upstream regulator gene (i.e., expressed gene) to any particular disease or condition that can be treated by a targeted drug to reverse differentially gene expression of said upstream regulator.
Alternatively, since it is known that diclofenac, dexamethasone, and prednisolone [Wiles, disclosure 0800] are utilized as anti-inflammatories, esters are used for their anti-inflammatory properties [disclosure 0829-0830] while myochrysine is utilized in the art for treating rheumatoid arthritis (RA) [Wiles, disclosure 0813], there is no correlation of treating the phenotype of corona virus with the targeted drug treatments in order to reverse differential gene expression of a specific phenotype.
Therefore, the administration of the targeted drug treatments and the targeted drug treatments of claims 37 and 45-46 do not integrate the recited judicial exception into a practical application because the claims do not recite limitations that have more than a nominal or insignificant relationship to the exception(s). See MPEP 2106.04(d)(2)(b).
Claim 32 recites the phenotype is associated with a coronavirus and administering a targeted treatment to treat the coronavirus. Claim 32 does not recite an additional element to which integrates the recited judicial exception claim 23 into a practical application because the administering of a treatment or prophylaxis limitations must have more than a nominal or insignificant relationship to the exception(s). The claim limitation must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. Thus, this administration step is not particular, and is instead merely instructions to "apply" the exception in a generic way. Therefore, the administration step does not integrate the mental analysis step into a practical application. See MPEP 2106.04(d)(2).
Claim 34 recites administering the targeted drug treatment to the subject includes administering a therapeutically effective amount of a first composition to the subject and administering a therapeutically effective amount of a second composition different from the first composition to the subject. Claim 34 does not recite an additional element to which integrates the recited judicial exception of claim 23 into a practical application because the claim limitation must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. Thus, this administration step is not particular, and is instead merely instructions to "apply" the exception in a generic way. Therefore, the administration step does not integrate the mental analysis step into a practical application. See MPEP 2106.04(d)(2).
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
2B Analysis: Consideration of Practical Application
The claimed method also recited “additional elements” that are not limitations drawn to abstract ideas.
The recited additional element of using a targeted drug treatment (i.e., the targeted drug treatment includes a composition comprising a compound selected from the group consisting of prednisolone, dexamethasone, diclofenac, myochrysine, esters thereof, derivatives thereof, salts thereof, and combinations thereof) of claims 23, 32, 34, 37, and 43-46 does not amount to more than the judicial exception because administering targeted drug treatments are well-known, routine, and conventional. To provide evidence of conventionality, Wiles et al. (Wiles) discloses using prednisolone [page 295 left col para 0800], dexamethasone [page 295 left col para 0800], diclofenac [page 295 left col para 0800], myochrysine [page 297 right col para 0813], and esters [page 29 left col 0338-0347]. Wiles discloses that the compounds can be to treat respiratory disease [page 23 left 0257]. Wiles discloses the compounds of the invention can be used to treat acute respiratory distress syndrome, adult respiratory distress syndrome [page 291 left col top para 0767]. Wiles discloses the drug of the invention can be used viral infection more generally, for example selected from Flaviviridae, Retroviruses, Coronaviridae, Poxviridae, Adenoviridae, Herpesviridae, Caliciviridae, Reoviridae, Picomaviridae, Togaviridae, Orthomyxoviridae, Rhabdoviridae, or Hepadnaviridae [page 289 right col para 0762] (Patent Pub: US 2020/0071301 Patent Pub Date: 05 March 2020).
To provide further evidence of conventionality, Wiles et al. (Wiles (2017)) discloses using prednisolone [col 65 lines 50-55], dexamethasone [col 65 lines 50-55], diclofenac [col 65 lines 60-65], myochrysine [col 67 lines 54-60], and ester [abstract]. Wiles (2017) discloses using the drugs for treating respiratory disease [col 13 lines 15-25] (US Patent: 9,732,103, Patent Date: 15 August 2017).
The recited additional element of administering a targeted treatment of claims 23, 34, 37, and 43-46 does not amount to more than the judicial exception because administering drug treatments are well-known, routine, and conventional.
The recited additional element of administering of claim 32 does not amount to more than the recited judicial exception because treating a subject with a coronavirus by administering drug treatments is well-known, routine, and conventional to perform the acts of administering a treatment. To exemplify conventionality of treating coronavirus with treatments, Zhou et al. (Zhou) teaches network-based drug repurposing for novel coronaviruses [title and abstract]. Zhou teaches a discovered subnetwork highlighting network-predicted drug-HCoV associations connecting 135 drugs and HCoVs [page 7 figure 4]. Zhou teaches a discovered drug-protein-HCoV network and 16 candidate repurposable drugs [page 8-9 fig 5] (Cell discovery, 2020-03, Vol.6 (1), p.14, Article 14).
In conclusion, when viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant’s arguments filed 25 August 2025, have been fully considered but the rejection is maintained. However, upon further consideration, a new ground(s) of rejection is made in view of the amendments filed 25 August 2025.
The Applicant states “