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 .
Claim Status
Original claims 1-20 filed 4/27/2023 are pending.
Priority
This application filed 4/27/2023 makes no claim for priority.
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 1-20 are rejected under 35 USC 101 because the claimed inventions are not directed to patent eligible subject matter. After consideration of relevant factors with respect to each claim as a whole, each claim is directed to one or more JEs (i.e. an abstract idea, a natural phenomenon, a law of nature and/or a product of nature), as identified below. Any elements or combination of elements beyond the JE(s) (i.e. "additional elements") are conventional and do not constitute significantly more than the JE(s). Thus, no claim includes additional elements amounting to significantly more than the JE(s), as explained below.
In Alice, citing Mayo and Bilski, two Mayo/Alice questions determine eligibility under 101: First, is a claim directed to a JE? And second, if so, does the claim recite significantly more than the JE?
MPEP 2106 organizes JE analysis into Steps 1, 2A (1st & 2nd prongs) and 2B as follows below.
MPEP 2106 and the following USPTO website provide further explanation and case law citations: www.uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter? -- MPEP 2106.I and 2106.03
[Step 1: claims 1-20: YES]
Step 2A, 1st prong: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea? -- abstract idea -- MPEP 2106.I and 2106.04
Preliminarily, in a 1st prong of Step 2A, elements of independent claim 1 are interpreted as directed to the abstract idea of identifying a change in a biological network including the JE elements of "construct...," "derive...," "determine an embedding vector...," "identify... changes in each sub-network...," "determine... scores..." and "identify... changes in the BN...," each of which, including all recitation within each listed element, in at least some embodiments within a BRI, involves only manipulation of data. While manipulation of data is not per se directed to an abstract idea, in this instance the above-identified elements are directed to the abstract ideas identified below. BRIs of the claims are analogous to an abstract idea in the form of at least a mental process, at least equivalent to a computer-implemented process, including obtaining and comparing intangible data (e.g. Cybersource, Synopsys and Electric Power Group). In a BRI, it is not clear that the claim embodiments are limited so as to require complexity precluding analogy to a mental process. BRIs of the claims also are analogous to an abstract idea in the form of a mathematical concept, including mathematical relationships and calculations, as found in the following case law, as cited and discussed above: collecting information, analyzing it, and displaying certain results of the collection and analysis (Electric Power Group) and/or obtaining and comparing intangible data (e.g. Cybersource, Ambry and Myriad CAFC) and/or execution of an algorithm to implement mathematical relationships and/or formulas, including image processing (e.g. TLI, Digitech, Benson, Flook, Diehr, FuzzySharp, In re Grams and In re Abele all as cited in MPEP 2106). Instant examples of math concepts include the recited embedding vector determination and determine scores, as well as relationships inherent in recitations as the only supported embodiments. The preceding case law examples are cited for the basic form of their identified abstract ideas, and analogy to these example abstract ideas need not be within the same technology field, 101 analysis generally being assumed to be neutral with respect to technology field. Regarding inherency of abstract ideas, MPEP 2106.04.II.A.1 includes: "the claims in Alice Corp. v. CLS Bank, 'described' the concept of intermediated settlement without ever explicitly using the words 'intermediated' or 'settlement'" (emphasis added, p. 1). Similarly, inherency can effectively be recitation, as in, for example, "By claiming simply 'crystalline paroxetine hydrochloride hemihydrate' with no reference to how it was produced, SKB effectively claimed 'crystalline paroxetine hydrochloride hemihydrate whether non-naturally occurring or arising through natural conversion.' Claim 1, as issued, therefore combines patentable and unpatentable subject matter, and is invalid under Section 101." (capitalization added, SmithKline Beecham Corp. v. Apotex Corp., 365 F.3d 1306, 1321-33, Fed. Cir. 2004).
In the instant type of data processing claims, the specification is not merely adding background explanation as to how a claimed process works, e.g. a physical process based on, involving or further explained by abstract ideas and natural laws. Rather, the specification is detailing the only disclosed way that a programmer may proceed from the recited inputs to the recited outputs, e.g. through actual performance of the disclosed judicial exceptions (JEs).
Regarding the "Meaning of 'Recites,'" MPEP 2106.04.II.A.1 states:
In Prong One examiners evaluate whether the claim recites a judicial exception, i.e. whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim. While the terms "set forth" and "described" are thus both equated with "recite", their different language is intended to indicate that there are two ways in which an exception can be recited in a claim. For instance, the claims in Diehr, 450 U.S. at 178 n. 2, 179 n.5, 191-92, 209 USPQ at 4-5 (1981), clearly stated a mathematical equation in the repetitively calculating step, and the claims in Mayo, 566 U.S. 66, 75-77, 101 USPQ2d 1961, 1967-68 (2012), clearly stated laws of nature in the wherein clause, such that the claims "set forth" an identifiable judicial exception. Alternatively, the claims in Alice Corp., 573 U.S. at 218, 110 USPQ2d at 1982, described the concept of intermediated settlement without ever explicitly using the words "intermediated" or "settlement."
While the "set forth" language approximates explicit recitation, it also is fundamental that all recitation must be interpreted and that to be patent eligible a claim must satisfy 101 according to its properly interpreted scope, e.g. for all embodiments on which the claim reads, e.g. according to any inherency pertinent to a given claim and disclosure accompanying that claim, i.e. consistent with the "described" meaning of "recites" as in the MPEP. Thus, within a BRI, the identified abstract idea elements read on one or more embodiments which only involve manipulation of data. It is not clear than any improvement argument clearly on the record causes a claim not to be directed to a JE for all embodiments within the scope of the claim.
As in Alice (at 306, as cited in the MPEP above) and Bilski (as cited in Alice, id), an abstract idea may comprise multiple abstract elements or steps (i.e. from Alice: "a series of steps" at 306) and need not be a single equation, relationship or principle.
It is not clear that the identified elements must represent other than an abstract idea according to any relevant analysis or case law.
[Step 2A, 1st prong, abstract idea: YES]
Step 2A, 2nd prong: If the claims recite a judicial exception under the 1st prong, then is the judicial exception integrated into a practical application? -- MPEP 2106.I and 2106.04(d)
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using 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, as discussed in MPEP § 2106.05(e).
In Step 2A, 1st prong above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In Step 2B below, any remaining steps and/or elements are therefore in addition to the identified JE(s). Any such additional steps and additional elements are further discussed in Step 2B.
Here in Step 2A, 2nd prong, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
At this point in examination, it is not yet the case that any of the Step 2A, 2nd prong considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of 1. an improvement, 2. treatment, 3. a particular machine or 4. a transformation is clear in the record.
For example, regarding the first consideration at MPEP 2106.04(d)(1), the record, including for example the specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field. The claims do not yet clearly result in such an improvement (e.g. specification: [5, 8, 23, 36]).
[Step 2A, 2nd prong: claims 1 and 8: NO]
Step 2B: Do the claims recite a non-conventional arrangement of additional elements in addition to the identified JEs? -- MPEP 2106.I and 2106.05
All elements of the claims 1 and 8 are part of a JE as identified above such that no element is recited which is additional to the identified JE(s). Therefore, no claim recites significantly more than the identified JE(s), and it is not clear that any claim is otherwise sufficiently analogous to controlling case law identifying an example of an eligible claim.
[Step 2B: claims 1 and 8: NO]
Summing up the above analysis of the claims each viewed as a whole and considering all elements individually and in combination, no claim recites limitations that transform the claim, finally interpreted as directed to the identified JE(s), into patent eligible subject matter, and it is not clear that any claim is sufficiently analogous to controlling case law identifying an example of an eligible claim.
Dependent claims add elements which also are part of the identified JEs for the same reasons described above regarding the independent claims and therefore do not provide the something significantly more necessary to satisfy 101.
None of the dependent claim elements provides the something significantly more than the identified JE(s) necessary to satisfy 101.
Claim rejections - 35 USC 103
In the event the determination of the status of the application as subject to AIA 35 USC 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.
The following is a quotation of 35 USC 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 of this title, 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.
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 USC 102(b)(2)(C) for any potential 35 USC 102(a)(2) prior art against the later invention.
Claims 1-20 are rejected under 35 USC 103 as unpatentable over Xia et al. and Emon et al. and Lavrac et al.
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. Xie teaches identifying known biological uses for matching proteins and query drugs, 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. 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. 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. Xie in view of teach the system and method of the independent claims while Emon teaches analyzing gene expression data (p. 12, par. 5) with SPIA (p. 15, par. 1-2).
With respect to claim 1 requirement of using a processor and relationship database for the analysis, the teachings of Lavrac et al. provide for a Biological Network with nodes, edges and sub-networks reads on "(heterogeneous) graphs" and "sub-networks" (Lavrac: abstract; §5.2.2, last para.; and entire chapter). The recited embedding vector reads on "node embeddings" (Lavrac: Fig. 5.4 caption; generally §5.2.3, last para.; and entire chapter). The recited identify a change by comparing reads on "graph comparison" (Lavrac: §5.1.1, last para.; and entire chapter). The recited node scoring reads on "node scoring" (Lavrac: §5.4.2, 2nd para. and generally; and entire chapter). The recited change identification reads on "the algorithm prunes the lower-ranked terms" and "Ontology Reduction" (Lavrac: Example 5.3, Step 3; §5.4.2 generally; and entire chapter). Lavrac also teaches "Network Node Removal" (Lavrac: §5.4.2.3; and entire chapter). Lavrac teaches each of the limitations as described above, however Lavrac does not teach the limitations in a single embodiment in the same, consecutive sequence as recited.
It would have been prima facie obvious to try the recited sequence as an example of combining prior art elements taught within the same reference according to known methods to yield predictable results. Lavrac teaches a summation of scores (Lavrac: equation 5.8; and entire chapter). Lavrac teaches at least one approach and one network type as "Biological networks" (Lavrac: §5.2.2; and entire chapter). Lavrac teaches "an embedding of dimension d" (Lavrac: Fig. 5.1 caption; and entire chapter). Lavrac teaches at least one of the recited types of change as "the algorithm prunes the lower-ranked terms" and "Ontology Reduction" (Lavrac: Example 5.3, Step 3; §5.4.2 generally; and entire chapter). Lavrac teaches a similarity measure as "node similarity" (Lavrac: p. 108, 2nd para.; and entire chapter).
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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/Joseph Woitach/Primary Examiner, Art Unit 1687
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