DETAILED ACTION
Comments
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 (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Claims 1-5, 7-12, and 14 are pending and examined in the instant Office action.
Claim Rejections - 35 USC § 112(b) - Indefiniteness
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.
The following rejections are reiterated:
Claims 1-5, 7-12, and 14 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.
Each of claims 1, 5, 8, and 12 do not state whether or not the limitations of the claims are recited in the alternative. For the purpose of examination, it is interpreted that the limitations of the claims are NOT recited in the alternative.
Each of claims 4 and 11 recite the use of publicly available database. It is unclear as to when the databases are publicly available. For example, it is unclear as to whether the databases are publicly available at the time of conception of the invention or at the time of the effective filing date of the application. For the purpose of examination, it is interpreted that the databases are publicly available at the time of the effective filing date of the application.
Each of claims 5 and 12 recite the term “phenotypic target” (singular) throughout the each of the claims. The only antecedent basis for “phenotypic target” (singular) is “phenotypic targets” (plural). It is unclear as to which of the “phenotypic targets” (plural) that the “phenotypic target” (singular) refers. For the purpose of examination, it is interpreted that “phenotypic target” (singular) can refer to any of the “phenotypic targets” (plural).
Each of claims 10-12 and 14 recites the limitation "a method according to claim 1" in line 1. There is insufficient antecedent basis for this limitation in the claim. Claim 1 is drawn to a system. For the purpose of examination, it is interpreted that “a method according to claim 1” corresponds to “a method according to claim 8”.
While the claims have been amended to have a limiting description of HDPA in that HDPA involves calculation of two distinct probabilities, it is unclear as to the roles of these probabilities in computing the mechanistic factors attributing to regulation of similar phenotypes and pathological information of the disease in association with the screened phenotypic targets.
While this passage indicates that HDPA takes into account differential expression of genes and fold change values, it is unclear as to the metes and bounds of the roles of differential expression of genes and fold change values in defining HDPA.
Response to arguments:
Applicant's arguments filed 17 August 2025 have been fully considered but they are not persuasive.
Applicant argues that the claims have been amended to requires that the limitations of the claim to NOT be recited in the alternative. This amendment has not been made to the claims.
While applicant gives examples of publicly available databases, applicant does not answer the indefiniteness questions regarding the times and breadth of availability of the “public” databases with respect to the time of the effective filing date of the instant application.
While applicant argues that claims 10-12 and 14 are amended, claims 10-12 and 14 are still in original form.
While applicant has amended the claims to have a limiting description of HDPA, the claims do not recite the metes and bounds of relating the probabilities to the objective of the claims.
Claim Rejections - 35 USC § 112(a) - Written Description
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.
The following rejection is necessitated by amendment:
Claims 1-5, 7-12, and 14 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.
While the claims have been amended to recite a limiting description of HDPA, the specification lacks support for this definition of HDPA.
Lines 16-21 of page 24 of the specification states, “Herein, HDPA takes into account data about differential expressions of genes, to gain mechanistic insights into the phenotypic targets that are observed. Furthermore, HDPA comprises fold change (FC) values, that indicates magnitude of change in gene expression, wherein the change in gene expression may be upregulated or downregulated.”
While this passage indicates that HDPA takes into account differential expression of genes and fold change values, the specification lacks possession of relating the two distinct mathematical probabilities to HDPA. Since the term HDPA is specific to this inventive entity and not a term known to one of skill in the art, this lack of possession amounts to NEW MATTER.
Response to arguments:
Applicant's arguments filed 17 August 2025 have been fully considered but they are not persuasive.
Applicant generally asserts that while the term “HDPA” is not a term of art, one of ordinary skill in the art should still understand the meaning of HDPA. Applicant gives no support for this general assertion. Applicant’s Remarks do not cite a portion of the specification where the recited definition of HDPA is disclosed.
Claim Rejections - 35 USC § 112(a) – Enablement
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.
The following rejection is reiterated:
Claims 1-5, 7-12, and 14 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
1. While the claims have been amended to have a limiting description of HDPA in that HDPA involves calculation of two distinct probabilities, it is not understood as to the roles of these probabilities in computing the mechanistic factors attributing to regulation of similar phenotypes and pathological information of the disease in association with the screened phenotypic targets.
2. The specification does not teach how to use an HDPA. Lines 16-21 of page 24 of the specification states, “Herein, HDPA takes into account data about differential expressions of genes, to gain mechanistic insights into the phenotypic targets that are observed. Furthermore, HDPA comprises fold change (FC) values, that indicates magnitude of change in gene expression, wherein the change in gene expression may be upregulated or downregulated.”
While this passage indicates that HDPA takes into account differential expression of genes and fold change values, the specification lacks a teaching of the roles of differential expression of genes and fold change values in defining HDPA. The term HDPA is specific to this inventive entity and not a term known to one of skill in the art.
3. The prior art teaches many ways to use differential gene expression and fold change to classify a disease ontology. For example, Figure 1 on page 532 of Golub et al. [Science, volume 286, 1999, pages 531-537] teaches using differential gene expression and fold change to classify a leukemia patient as having ALL or AML.
4. The term HDPA is not common to one of skill in the art. While the claims relate HDPA to two distinct probabilities, the claims do not teach the roles of these probabilities in fulfilling the objectives of the claims. While the specification relates differential gene expression and fold change to HDPA, the specification does not teach explicitly how to explicitly use differential gene expression and fold change to calculate HDPA. While the prior art teaches many ways to use differential gene expression and fold change to classify gene ontology, it is unpredictable is to which of the many algorithms constitute an HDPA. This unpredictability yields UNDUE EXPERIMENTATION.
In view of the above, it is the Examiner’s position that with the insufficient guidance and working examples and in view of unpredictability and the state of art, one of skill in the art could not make and/or use the invention with the claimed breadth without an undue amount of experimentation.
Response to arguments:
Applicant's arguments filed 17 August 2025 have been fully considered but they are not persuasive.
While the Remarks attempt to explain the claims and generally relate the Wands factors to the claims, the claims do not teach how to use the claims, specification, or prior art to relate the two probabilities recited in the claims to computing the mechanistic factors attributing to regulation of similar phenotypes and pathological information of the disease in association with the screened phenotypic targets.
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.
The following rejection is reiterated:
Claim(s) 1-5, 7-12, and 14 is/are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. Claims 1-5 and 7 are drawn to systems comprising processors, and claims 8-12 and 14 are drawn to methods.
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1 : YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claims 1 and 8 recite the mental step of using a phenotype ontological databank comprising information pertaining to a plurality of phenotypes and phenotypic targets associated with each of the plurality of phenotypes.
Claims 1 and 8 recite the mental step of receiving a name of the disease as a first input.
Claims 1 and 8 recite the mental step of receiving at least one phenotype associated with the disease as a second input.
Claims 1 and 8 recite the mental step of identifying for each of the at least one phenotype a plurality of similar phenotypes relating to a particular phenotype of the at least one phenotype of the second input.
Claims 1 and 8 recite the mental step of determining a similarity score for each of the plurality of similar phenotypes in comparison with the particular phenotype of the at least one phenotype of the second input.
Claims 1 and 8 recite the mental step of extracting, from the phenotype ontological databank, phenotypic targets associated with similar phenotypes having similarity score higher than a first predefined threshold.
Claims 1 and 8 recite the mental step of computing a cumulative score of the phenotypic targets based on a plurality of parameters, wherein the cumulative score of a given phenotypic target is indicative of relevance with respect to the disease.
Claims 1 and 8 recite the mental step of screening out phenotypic targets with cumulative score lower than a second predefined threshold.
Claims 1 and 8 recite the mental step of computing pathways for the phenotypic targets by performing HDPA for the screened phenotypic targets.
Claims 1 and 8 recite the mental step of computing mechanistic factors attributing to regulation of similar phenotypes and pathological information of the disease in association with the screened phenotypic targets.
Claims 1 and 8 recite mathematical expressions in an attempt to define HDPA.
Claims 2 and 9 recite the mental step of selecting a disease name from a list of disease names.
Claims 3 and 10 recite the mental step of constraining at least one phenotype to be a cellular, molecular, or clinical phenotype.
Claims 4 and 11 recites the mental step of constraining the phenotype ontological databank to comprise a plurality of databases.
Claims 5 and 12 recite the mental steps of constraining the plurality of parameters to compute the cumulative score of the phenotypic target to comprise of a list of parameters.
Claims 6 and 13 recite the mental step of constraining the HDPA to use differential expression analysis of screened phenotypic targets.
Claims 7 and 14 recite the mental step of constraining forming a PTP network using interactions between the screened phenotypic targets and most impacted pathways obtained from the results of HDPA.
These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claim(s) 1-5, 7-12, and 14 recite(s) an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 1 : YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or mere instructions to apply the recited judicial exception via a generic treatment.
As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. As such, claims 1-5, 7-12, and 14 is/are directed to an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 2 : NO).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
As discussed above, there are no additional limitations to indicate that the claimed analysis engine requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B : No). As such, claims 1-5, 7-12, and 14 is/are not patent eligible.
Response to arguments:
Applicant's arguments filed 17 August 2025 have been fully considered but they are not persuasive.
On page 5 of the Remarks, applicant explains the independent claims.
On page 6 of the Remarks, applicant argues that the claims do not recite mental steps by citing limitations, such as nodes, edges, and adjacency, which are not recited in the claims.
On page 6 of the Remarks, applicant generally asserts that the mathematics recited in the claims do not involve judicial exceptions. This argument is not persuasive because applicant gives no support for this general assertion.
On pages 6-7 of the Remarks, applicant argues that the probabilities calculated in claims result in the practical application of an improvement to technology. In view of the 35 U.S.C. 112 rejections above, it is unclear and not understood as to how these probability calculations result in an improvement to drug-discovery informatics.
On pages 7-8 of the Remarks, applicant argues that the ordered combination of elements, in combination with the specific mathematics of the amended claims result in subject matter that is not routine and conventional. This argument is not persuasive because the test of well-understood, routine, and conventional is typically applied to limitations outside the judicial exceptions. Since the claims have no limitations outside the judicial exceptions, this argument is not persuasive.
E-mail Communications Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Russell Negin, whose telephone number is (571) 272-1083. This Examiner can normally be reached from Monday through Thursday from 8 am to 3 pm and variable hours on Fridays.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s Supervisor, Larry Riggs, Supervisory Patent Examiner, can be reached at (571) 270-3062.
/RUSSELL S NEGIN/Primary Examiner, Art Unit 1686 11 November 2025