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 .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Claim Status
Claims 1-12 are pending.
Claims 1-12 are objected to.
Claims 1-12 are rejected.
Priority
The instant Application was filed Mar 8 2022 and does not claim the benefit of an earlier filed application.
Accordingly, each of claims 1-12 are afforded the effective filing date of Mar 8 2022.
Information Disclosure Statement
The information disclosure statement (IDS) filed on Mar 8 2022 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS document is included with this Office Action.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: 308 in FIG. 3.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they do not include the following reference sign(s) mentioned in the description: system 300 mentioned on p. 20, line 15.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to for the following informalities. It is noted that for purposes of the instant Office Action, any reference to the specification pertains to the specification as originally filed on Mar 8 2022.
Title
The title of the invention is objected to because it should be amended to “SYSTEM AND METHOD FOR GAINING MECHANISTIC INSIGHTS INTO AN ACTION OF A DRUG USING IN-SILICO TECHNIQUES” or “SYSTEM AND METHOD FOR GAINING MECHANISTIC INSIGHTS INTO ACTIONS OF DRUGS USING IN-SILICO TECHNIQUES”.
Disclosure
35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, requires the specification to be written in “full, clear, concise, and exact terms.” The specification is replete with terms which are not clear, concise and exact. The specification should be revised carefully in order to comply with 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112. Examples of some unclear, inexact or verbose terms used in the specification are: “Conventionally, (the) process of drug discovery”; “thereby enabling to gain mechanistic insights”; and “wherein the in-vitro techniques are unable to screen the multiple phenotypes and phenotypic targets at a single,” on p. 1, lines 9-20. It is noted that these are only exemplary instances.
Appropriate correction for all objections to the specification is required.
Claim Objections
The claims are objected to for the following informalities:
Claim 1 recites “A system for gaining mechanistic insights into action of a drug”, which should be amended to recite “into an action” or “actions”. Claim 7 is similarly objected to.
Claim 1, line 8, recites “receive a name the drug”, which should be amended to recite “receive a name of the drug”.
Claim 1, line 12, recites “determine, phenotypes”. The comma should be removed. Claim 7 is similarly objected to.
Claim 1, line 22, recites “analysis of PTP network”, which should be amended to recite “the PTP network”. Claim 7 is similarly objected to.
Claims 1 and 7 are both missing an “and” at the end of the second to last limitation.
Claims 2-6 recite “A system of claim 1” and claims 8-12 recite “A method of claim 7”. Claims 2-6 should be amended to recite “[[A]] The system of claim 1” and claims 8-12 should be amended to recite “[[A]] The method of claim 7”.
Claim 3 recites “to use chemical similarity algorithm”, which should be amended to recite “to use a chemical similarity algorithm”. Claim 9 is similarly objected to.
Claim 4 recites “to use molecular docking method”, which should be amended to recite “to use a molecular docking method”. Claim 10 is similarly objected to.
Claim 6 recites “Signaling Pathway Impact Analysis (SPIA)”, which should be amended to recite only “SPIA” because the term was previously introduced in claim 1 as SPIA. Claim 12 is similarly objected to.
Claim Rejections - 35 USC § 112
35 U.S.C. 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-12 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 1, line 10, recites “fetch targets of at least one existing drug that is similar to the drug”. The term “similar” in claim 1 is a relative term which renders the claim indefinite. The term “similar” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Therefore, the scope of existing drug is unclear. Claim 7 is similarly rejected. Claims 2-6 and 8-12 are rejected based on their dependency from claims 1 and 7.
Claim 1, line 15, recites “the phenotypic targets of the drug”. There is insufficient antecedent basis for this limitation in the claim as there is no previous recitation of phenotypic targets of the drug. It is therefore also not clear what is being compared with the drug target list to identify a plurality of overlapping targets in lines 15-16 because the claim does not introduce or describe the phenotypic targets. Because the scope of the overlapping targets is unclear, the limitation of “compute relevant pathways by performing… SPIA for the plurality of overlapping targets” in lines 18-19 is also unclear. For compact examination, any art that teaches comparing lists or networks of protein and drug interactions will be considered relevant. The rejection may be overcome by clarifying the antecedent basis of the limitation. Claim 7 is similarly rejected. Claims 2-6 and 8-12 are rejected based on their dependency from claims 1 and 7.
Claim 1, line 22, recites “the analysis of PTP network”. There is insufficient antecedent basis for this limitation in the claim as there is no previous recitation of an analysis of the PTP network, only the generation of the PTP network in the previous limitation. It is therefore not clear if the claim intends for the mechanistic insight to be computed as a byproduct of performing an analysis of the PTP network, or if an analysis of the network is not required to be performed, but the results of such an analysis are used to then compute mechanistic insights. For compact examination, it is assumed that the claim intends to recite “computing mechanistic insights into the action of the drug from [[the]] analysis of the PTP network” or “by analyzing the PTP network”. The rejection may be overcome by clarifying the metes and bounds of the claim. Claim 7 is similarly rejected. Claims 2-6 and 8-12 are rejected based on their dependency from claims 1 and 7.
Claim 3 recites “the… unknown drugs”. There is insufficient antecedent basis for this limitation in the claim as there is no previous recitation of unknown drugs. It is not clear if the limitation is intended to further limit the drug of claim 1 to an unknown drug, or if it intends to refer to a separate drug which is unknown. The rejection may be overcome by clarifying the antecedent basis of the limitation. Claim 9 is similarly rejected.
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 1-12 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to a system and a method, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) are as follows:
Independent claims 1 and 7: determine phenotypes of the drug based on associations between the targets in the drug target list and the phenotypes;
compare the drug target list with the phenotypic targets of the drug to identify a plurality of overlapping targets therebetween;
generate a network comprising the drug, the targets and the phenotypes;
compute relevant pathways by performing Signaling Pathway Impact Analysis (SPIA) for the plurality of overlapping targets;
generate a Pathway-Target-Phenotype (PTP) network using the most impacted pathways obtained from the results of SPIA;
compute mechanistic insights into the action of the drug from the analysis of PTP network.
Dependent claims 2 and 8: use literature mining to fetch drug targets of known drugs.
Dependent claims 3 and 9: use chemical similarity algorithm to identify the at least one existing drug that is similar to the drug and/or unknown drugs.
Dependent claims 4 and 10: … to predict targets of the at least one drug to obtain the drug target list.
Dependent claims 5 and 11: select the second input relating to at least one phenotype associated with the drug from within a list of phenotypes.
Dependent claims 6 and 12 recite further steps that limit the judicial exceptions in independent claim 1 and 7 by further limiting the performance of SPIA, and, as such, also are directed to those abstract ideas.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually determine mechanistic insights into the action of a drug based on associations between targets and phenotypes of similar drugs. Without further detail as to the methodology involved in “determining”, “comparing”, “generating”, “comparing”, and “computing”, under the BRI, one may simply, for example, use pen and paper to determine similar drugs to a first drug, select phenotypes of the drug from a list, identify or predict drug targets in the literature or from molecular docking results, record targets of an existing drug, record phenotypes associated with targets based on their presence in a databank, compare lists of targets and phenotypes, generate a network by drawing nodes and connections between a drug and a list of targets and phenotypes, use Signaling Pathway Impact Analysis (SPIA) based on differential expression of the targets to identify relevant pathways, generate a Pathway-Target Phenotype network by drawing nodes and connections based on the pathways identified with SPIA, and determine mechanistic insights into the drug by analyzing the PTP network. Some of these steps and those recited in the dependent claims, like SPIA and differential expression analysis, require mathematical techniques as the only supported embodiments, as is disclosed in the specification at: p. 16, line 3 through p. 17, line 5.
Therefore, claims 1 and 7 and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Independent claims 1 and 7: receive a name the drug as a first input;
receive a second input relating to at least one phenotype associated with the drug; and
fetch targets of at least one existing drug that is similar to the drug to obtain a drug target list.
Dependent claims 4 and 10: use molecular docking method…
The claims also include non-abstract computing elements. For example, independent claims 1 and 7 include a system communicably coupled to a phenotype ontological databank and comprising a processor communicably coupled to a memory, the processor configured to perform the method.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “use molecular docking” in claims 4 and 10 and “receiving” and “fetching” data, perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering and outputting steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
Further steps directed to additional non-abstract computing elements do not describe any specific computational steps by which the “computer parts” perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
The specification discloses that the invention is intended to overcome drawback associated with known techniques for gaining mechanistic insight into the action of a drug at p. 1, lines 24-26, but does not provide a clear explanation for how the additional elements provide these improvements. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the specification discloses that molecular docking is a data gathering element that is routine, well-understood and conventional in the art which is performed using known docking engines like DOCK and AutoDOCK. Said portions of the prior art are, for example, p. 12, line 16 through p. 13, line 6. Further, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(II)(i)). As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
With respect to claims 1 and 7 and those claims dependent therefrom, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (Alice Corp., 573 U.S. at 225-26, 110 USPQ2d at 1984; see MPEP 2106.05(A)). The specification also notes that computer processors and systems, as example, are commercially available or widely used at p. 7. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
A. Claims 1, 3, 5-7, 9, and 11-12 are rejected under 35 U.S.C. 103 as being unpatentable over Xia et al. (US 2016/0171173; newly cited) in view of Emon et al. (BMC Bioinformatics, 2020 21(1), p.231; newly cited).
Claim 1 discloses a system for gaining mechanistic insights into action of a drug using in-silico techniques, the system is communicably coupled to a phenotype ontological databank comprising information pertaining to a plurality of drugs and the corresponding targets thereof; wherein the system comprises a processor communicably coupled to a memory, the processor configured to receive a name the drug as a first input; receive a second input relating to at least one phenotype associated with the drug; fetch targets of at least one existing drug that is similar to the drug to obtain a drug target list; determine, phenotypes of the drug based on associations between the targets in the drug target list and the phenotypes, said associations being accessed from the phenotype ontological databank; compare the drug target list with the phenotypic targets of the drug to identify a plurality of overlapping targets therebetween; generate a network comprising the drug, the targets and the phenotypes; compute relevant pathways by performing Signaling Pathway Impact Analysis (SPIA) for the plurality of overlapping targets; generate a Pathway-Target-Phenotype (PTP) network using the most impacted pathways obtained from the results of SPIA; compute mechanistic insights into the action of the drug from the analysis of PTP network. Claim 7 discloses a computer-implemented method for gaining mechanistic insights into action of a drug using in-silico techniques, wherein the method is implemented using a system communicably coupled to a phenotype ontological databank comprising information pertaining to a plurality of drugs and the corresponding targets thereof; wherein the system comprises a processor communicably coupled to a memory, the method comprising: receiving a name of the drug as a first input; receiving a second input relating to at least one phenotype associated with the drug; fetching targets of at least one existing drug that is similar to the drug to obtain a drug target list; determining, phenotypes of the drug based on associations between the targets in the drug target list and the phenotypes, said associations being accessed from the phenotype ontological databank; comparing the drug target list with the phenotypic targets of the drug to identify a plurality of overlapping targets therebetween;- generating a network comprising the drug, the targets and the phenotypes; computing relevant pathways by performing Signaling Pathway Impact Analysis (SPIA) for the plurality of overlapping targets; - generating a Pathway-Target-Phenotype (PTP) network using the most impacted pathways obtained from the results of SPIA; computing mechanistic insights into the action of the drug from the analysis of PTP network.
Regarding claims 1 and 7, the prior art to Xie discloses a method for identifying new uses of known drugs is disclosed (abstract). Xie teaches that the invention may be embodied as a system, method, or computer program product [0039]. Xie provides a systems pharmacology paradigm for drug discovery which focuses on searching for multi-target drugs to perturb diseased-associated networks rather than designing a selective ligand to target an individual receptor [0014]. With respect to the limitations of claims 1 and 8 in which an input drug is received Xie shows given a query drug, the query drug is linked to the drug similarity network by the chemical similarity [0018]. Xie shows output of the algorithm is the list of all proteins in the network (or a subset thereof), ranked by the probability py for the query chemical to reach the protein [0018], reading on fetching targets of similar drugs. Xie shows functional similarity (phenotypes) is evaluated by semantic similarity of Gene Ontology (GO) terms [0023], which reads on the second input of at least one phenotype associated with the drug and determining phenotypes based on association from an ontological database. With respect to the limitation of generating a network comprising the drug, target and phenotype, Xie shows a drug-target coherent ranking is assessed for each pair of drug-drug and protein-protein similarity networks [0024], which also reads on comparing the drug target list with the phenotypic targets of the drug to identify a plurality of overlapping targets therebetween as instantly claimed, in view of the above described 35 USC 112(b) rejection. Xie teaches identifying known biological uses for matching proteins and query drugs (claim 1), which reads on computing mechanistic insights into the action of the drug as instantly claimed.
Xie does not teach computing relevant pathways by performing SPIA, generating a Pathway-Target-Phenotype (PTP) network using the most impacted pathways obtained from the results of SPIA, or computing mechanistic insights into the action of the drug from the analysis of PTP network.
However, the prior art to Emon discloses a customizable workflow to integrate high-throughput gene expression data such as signatures from disease and drug perturbations with pathway knowledge to predict drug candidates for repositioning (abstract), where new indications for approved drugs are identified (p. 2, par 1). Emon teaches performing Signaling Pathways Impact Analysis (SPIA) on three pathway databases for “drug-specific gene sets in disease” which gives signed pathway dysregulation for all available drugs (p. 15, par. 2). Emon teaches performing drug prioritization that uses the results of pathway enrichment methods to prioritize drugs based on how well they can counteract the overall pathway signatures on each disease (i.e., computing mechanistic insights into the action of the drug) by considering only statistically significant pathways (i.e., a PTP network with only the most impacted pathways obtained from SPIA) (p. 15, par. 3 through p. 17, par. 1).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Xie and Emon because both references disclose methods for identifying new uses of known drugs. The motivation to use SPIA to analyze the drug target list of Xie would have been to use a method which uses drug-based and disease-based data for drug repositioning purposes, as taught by Emon (p. 2, par. 2), which would have produced the predictable result of identifying the mechanism of action of a drug based on its similarity to other known drugs.
Regarding claims 3 and 9, Xie in view of teach the system and method of claims 1 and 7. Claims 3 and 9 further add using chemical similarity algorithm to identify the at least one existing drug that is similar to the drug and/or unknown drugs.
Xie shows given a drug database comprising chemical similarity data concerning a plurality of drugs and evaluating statistically significant chemical similarity between the drugs [0018; 0026], which reads on using a chemical similarity algorithm as instantly claimed.
Regarding claims 5 and 11, Xie in view of teach the system and method of claims 1 and 7. Claims 5 and 11 further add selecting the second input relating to at least one phenotype associated with the drug from within a list of phenotypes.
Xie teaches functional similarity (phenotypes) is evaluated by semantic similarity of Gene Ontology (GO) terms [0023], which reads on electing the second input relating to at least one phenotype associated with the drug from within a list of phenotypes as instantly claimed.
Regarding claims 6 and 12, Xie in view of teach the system and method of claims 1 and 7. Claims 6 and 12 further add performing Signaling Pathway Impact Analysis (SPIA) using differential expression analysis of the plurality of overlapping targets, which Xie does not teach.
However, Emon teaches analyzing gene expression data (p. 12, par. 5) with SPIA (p. 15, par. 1-2).
B. Claims 2, 4, 8, and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Xie in view of Emon, as applied to claims 1 and 7 as above, and in further view of Manivannan et al. (RSC Advances, 2015, 5(94), pp.77042-77055; newly cited).
Regarding claims 2 and 8, Xie in view of teach the system and method of claims 1 and 7. Claims 2 and 8 further add using literature mining to fetch drug targets of known drugs, which Xie does not teach.
Regarding claims 4 and 10, Xie in view of teach the system and method of claims 1 and 7. Claims 4 and 10 further add using molecular docking method to predict targets of the at least one drug to obtain the drug target list, which Xie does not teach.
However, the prior art to Manivannan discloses predicting targets of compounds by reverse pharmacophore and structural similarity based target-screening methods, exploring compound–target pathways (Biocarta and KEGG) and disease relationships, prioritizing important pathogenic targets using microarray transcriptomic data, and exploring the interaction of the compounds on the targets via docking (i.e., molecular docking) (abstract; p. 77045, col. 1, par. 2-3. Manivannan teaches identifying compound-target interactions using text mining (i.e., literature mining) and STITCH information about compound-target interactions (Table 6; Section 3.4).
Regarding claims 2, 4, 8, and 10, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Xie in view of Emon with Manivannan because each reference discloses methods for identifying new uses of known drugs. Although Manivannan did not explicitly teach using molecular docking to predict targets in their study, they note that molecular docking has been used as a virtual screening method previously (p. 77050, col. 2, par. 2), which they chose not to do in order to re-validate compound-target associations (p. 77043, col. 2, par. 1). However, it would have been obvious to perform the re-validation with molecular docking simulations, as has been done previously (p. 77050, col. 2, par. 2). The motivation to use molecular docking or literature mining would have been to provide an essential virtual screening method to identify targets for compounds, as taught by Manivannan (p. 77050, col. 2, par. 2).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1-12 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 and 8 of copending Application No. 17539626 in view of Emon et al. (BMC Bioinformatics, 2020 21(1), p.231; newly cited).
This is a provisional nonstatutory double patenting rejection.
Regarding claims 1 and 7, reference claims 1 and 8 disclose the limitations of the claims except for the limitations “compute relevant pathways by performing Signaling Pathway Impact Analysis (SPIA) for the plurality of overlapping targets” and “generate a Pathway-Target-Phenotype (PTP) network using the most impacted pathways obtained from the results of SPIA”.
However, the prior art to Emon discloses a customizable workflow to integrate high-throughput gene expression data such as signatures from disease and drug perturbations with pathway knowledge to predict drug candidates for repositioning (abstract), where new indications for approved drugs are identified (p. 2, par 1). Emon teaches performing Signaling Pathways Impact Analysis (SPIA) on three pathway databases for “drug-specific gene sets in disease” which gives signed pathway dysregulation for all available drugs (p. 15, par. 2). Emon teaches performing drug prioritization that uses the results of pathway enrichment methods to prioritize drugs based on how well they can counteract the overall pathway signatures on each disease (i.e., computing mechanistic insights into the action of the drug) by considering only statistically significant pathways (i.e., a PTP network with only the most impacted pathways obtained from SPIA) (p. 15, par. 3 through p. 17, par. 1).
Regarding claims 2-4 and 8-10, reference claim 1, limitation 3, and claim 8, limitation 2, disclose the limitations of the claims.
Regarding claims 5 and 11, reference claims 1 and 8 disclose the limitations of the claims in at least the phenotype ontological databank.
Regarding claims 6 and 12, the reference claims do not disclose the limitations of the claims.
However, Emon teaches analyzing gene expression data (p. 12, par. 5) with SPIA (p. 15, par. 1-2).
Regarding claims 1-12, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Emon because both references disclose methods for identifying new uses of known drugs. The motivation to use SPIA to analyze the drug target list of Xie would have been to use a method which uses drug-based and disease-based data for drug repositioning purposes, as taught by Emon (p. 2, par. 2), which would have produced the predictable result of identifying the mechanism of action of a drug based on its similarity to other known drugs.
Conclusion
No claims are allowed.
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/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685