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 .
Claim Status
Claims 1-15 are currently pending and under examination herein.
Claims 1-15 are rejected.
Priority
The application claims benefit of provisional application: 62/165,879 priority, filing date 05/22/2015, and is acknowledged. This is a 371 of PCT/CA2016/050581, filed 05/20/2016, and a CON of 15/576,520 (US Patent No. 11,515,004), filed 04/20/2018.
In this action, all claims 1-15 are examined for an effective filing date of 05/22/2015. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further analysis of the disclosure(s) of the priority application(s).
Information Disclosure Statement
Information Disclosure Statements, two filed 09/14/2023, have been considered. Signed copies of the IDS are included with this Office Action
.
Drawings
The Drawings submitted 09/14/2023 are accepted. The drawings as filed are suitable to the Examiner. Applicant is encouraged to review the submission in PAIR to ensure all details are readable, particularly Fig 9.
Objections: Specification
The disclosure is objected to because:
page 16 has elements generally determined to be figures (a histogram, and two network diagrams), and not tables (lists of numerical data). These should be converted to figures, added, and properly described in the “Brief Description of the Figures” section, as required.
it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. See at least page 10 of the substitute specification.
Claim Objections
Claims are objected to because of the following informalities:
Claim 6 fails to end with a period as required (after the final equation).
Appropriate correction is required.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier.
Such claim limitation(s) is/are:
“computing…a thermodynamic measure for each protein node…” in claim 1;
“generating an energy landscape data corresponding to the network of protein nodes and the thermodynamic measure” in claim 1;
“generating a PPI subnetwork by applying a topological filtration” in claim 1;
“Computing” is the generic placeholder, and each function is the specialized function.
“processing circuitry configured to execute instructions to:
“compute… a thermodynamic measure for each protein node…” in claim 12;
“generate an energy landscape data corresponding to the network of protein nodes and the thermodynamic measure” in claim 12;
“generate a PPI subnetwork by applying a topological filtration” in claim 12.
“Processing circuitry configured to” is the generic placeholder. Each function is the specialized function.
“instructions…that…cause the computer to perform operations comprising: computing…a thermodynamic measure for each protein node…” in claim 14;
“generating an energy landscape data corresponding to the network of protein nodes and the thermodynamic measure” in claim 14;
“generating a PPI subnetwork by applying a topological filtration” in claim 14;
“Instructions” which cause the computing is the generic placeholder, and each function is the specialized function.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112
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 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 1-15 are rejected under 35 USC 112 2nd or 112(b) as failing to particularly point out and distinctly claim the invention. Claims 1-15 fail to particularly point out and distinctly claim the subject matter which applicant regards as his invention.
Claim limitation “computing…a thermodynamic measure for each protein node…” in claims 1 and 14 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The claims fail to particularly set forth and distinctly claim the actual algorithms, step-by-step processes or structures required to compute the thermodynamic measure using the unspecified genomic information and unspecified PPI data. The claim fails to set forth how to apply any unspecified genomic information to a generic PPI network to achieve a thermodynamic measure for each unspecified protein node. The claim fails to identify what genomic material is relevant, necessary and sufficient for the stated goals. The claim fails to particularly set forth how to incorporate any genomic information into a thermodynamic calculation which represents some aspect of a protein-protein interaction network node. A reading of the specification provides a variety of possibilities, however no specific definition or calculation which is necessary and sufficient is provided. While the claims are read in light of the specification, limitations from the specification cannot be read into the claims.
Claim limitation “generating an energy landscape data corresponding to the network of protein nodes and the thermodynamic measure” in claims 1 and 14 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The claims fail to particularly set forth and distinctly claim the algorithms, step-by-step procedures or structures which are necessary and sufficient to achieve an “energy landscape corresponding to the network of protein nodes and the thermodynamic measure” as required. The metes and bounds of the term “energy landscape” are unclear, and the specification fails to provide a particular, specific definition of how is it to be “generated” based on the information provided. While claims are read in light of the specification, limitations from the specification cannot be read into the claims.
Claim limitation “generating a PPI subnetwork by applying a topological filtration” in claims 1 and 14 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The claims fail to particularly point out and distinctly claim the algorithms, step-by-step processes or structures required to generate a subnetwork by “applying” an unspecified topological filtration. While claims are read in light of the specification, limitations from the specification cannot be read into the claims.
Claim limitation “processing circuitry configured to execute instructions to: “compute… a thermodynamic measure for each protein node…” in claim 12 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The claims fail to particularly set forth and distinctly claim the actual algorithms, step-by-step processes or structures required to compute the thermodynamic measure using the unspecified genomic information and unspecified PPI data. The claim fails to set forth how to apply any unspecified genomic information to a generic PPI network to achieve a thermodynamic measure for each unspecified protein node. The claim fails to identify what genomic material is relevant, necessary and sufficient for the stated goals. The claim fails to particularly set forth how to incorporate any genomic information into a thermodynamic calculation which represents some aspect of a protein-protein interaction network node. A reading of the specification provides a variety of possibilities, however no specific definition or calculation which is necessary and sufficient is provided. While the claims are read in light of the specification, limitations from the specification cannot be read into the claims.
Claim limitation “generate an energy landscape data corresponding to the network of protein nodes and the thermodynamic measure” in claim 12 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The claims fail to particularly set forth and distinctly claim the algorithms, step-by-step procedures or structures which are necessary and sufficient to achieve an “energy landscape corresponding to the network of protein nodes and the thermodynamic measure” as required. The metes and bounds of the term “energy landscape” are unclear, and the specification fails to provide a particular, specific definition of how is it to be “generated” based on the information provided. While claims are read in light of the specification, limitations from the specification cannot be read into the claims.
Claim limitation “generate a PPI subnetwork by applying a topological filtration” in claim 12 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The claims fail to particularly point out and distinctly claim the algorithms, step-by-step processes or structures required to generate a subnetwork by “applying” an unspecified topological filtration. While claims are read in light of the specification, limitations from the specification cannot be read into the claims.
MPEP 2181.II.B: “For a computer-implemented 35 U.S.C. 112(f) claim limitation, the specification must disclose an algorithm for performing the claimed specific computer function, or else the claim is indefinite under 35 U.S.C. 112(b) (b). See Net MoneyIN, Inc. v. Verisign. Inc., 545 F.3d 1359, 1367 (Fed. Cir. 2008).”
“To claim a means for performing a specific computer-implemented function and then to disclose only a general purpose computer as the structure designed to perform that function amounts to pure functional claiming. Aristocrat, 521 F.3d 1328 at 1333, 86 USPQ2d at 1239.”
“Mere reference to a general purpose computer with appropriate programming without providing an explanation of the appropriate programming, or simply reciting "software" without providing detail about the means to accomplish a specific software function, would not be an adequate disclosure of the corresponding structure to satisfy the requirements of 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. Aristocrat, 521 F.3d at 1334, 86 USPQ2d at 1239...”
Therefore, claims 1-15 are indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
Claims 1-15 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 WRITTEN DESCRIPTION rejection.
As set forth above, the claims invoke 112 6th paragraph for the three specific steps related to the thermodynamic measure, the energy landscape, and the topological filtration. The specification fails to specifically disclose the necessary and sufficient algorithms, step-by-step procedures or structures required to compute or generate each specialized function, and fails to specifically link those structures to the specialized functions of the claims. Merely stating the desired goal of the step is not a written description of the actual steps required to achieve the goal. While the specification recites a variety of algorithms, it is the specific linkage of a particular set of steps which are necessary and sufficient to achieve each specialized function that are lacking.
MPEP 2181.II.B: “For a computer-implemented 35 U.S.C. 112(f) claim limitation, the specification must disclose an algorithm for performing the claimed specific computer function, or else the claim is indefinite under 35 U.S.C. 112(b) (b). See Net MoneyIN, Inc. v. Verisign.Inc., 545 F.3d 1359, 1367 (Fed. Cir. 2008).”
“To claim a means for performing a specific computer-implemented function and then to disclose only a general purpose computer as the structure designed to perform that function amounts to pure functional claiming. Aristocrat, 521 F.3d 1328 at 1333, 86 USPQ2d at 1239.”
“Mere reference to a general purpose computer with appropriate programming without providing an explanation of the appropriate programming, or simply reciting "software" without providing detail about the means to accomplish a specific software function, would not be an adequate disclosure of the corresponding structure to satisfy the requirements of 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. Aristocrat, 521 F.3d at 1334, 86 USPQ2d at 1239...”
“When a claim containing a computer-implemented 35 U.S.C. 112(f) claim limitation is found to be indefinite under 35 U.S.C. 112(b) for failure to disclose sufficient corresponding structure (e.g., the computer and the algorithm) in the specification that performs the entire claimed function, it will also lack written description under 35 U.S.C. 112(a). See MPEP § 2163.03, subsection VI.”
Claims 1-15 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.
The metes and bounds of the final “determining” step are unclear. The claim fails to particularly point out how any change in the Betti numbers is related to significance of a protein target in the subnetwork. There are no steps or limitations which indicate what type of change or degree of change is associated with “significance”. This applies equally to claims 12 and 14.
The term "most significant protein target" in claim 1 is a relative term which renders the claim indefinite. The term "most significant" 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. It is entirely unclear how to determine what protein node may or may not achieve significance given the information provided. This applies equally to claims 2, 12 and 14-15.
The metes and bounds of claim 3 are unclear, as it is unclear where within claim 1 this limitation is to be applied, and it is further unclear how it affects the method of claim 1. It does not appear to actually further limit any method steps.
The metes and bounds of claim 4 are unclear, as the claim fails to set forth what information is within the database, merely the location of it. It does not appear to clearly further limit claim 1 with any information which can be applied to the method steps.
The metes and bounds of claim 5 are unclear. The claim, while listing two types of transcription data, fails to particularly point out how that transcription data is to be applied to a calculation of a thermodynamic measure, as required.
The metes and bounds of claim 6 are similarly unclear. While the claim states the thermodynamic measure is “computed using the transcription data and an equation….” it fails to particularly point out how the transcription data is applied. Merely “using” that data is not a specific, clearly defined step. Claim 6 fails to set forth a definition of each variable of the two equations.
The metes and bounds of claim 7 are entirely unclear. The term "persistent homology" in claim 7 is a relative term which renders the claim indefinite. The term "persistent homology" 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. The limitation following the term “that is extracted from the energy landscape of the PPI data using the topological filtration” fails to provide any positive active method step by which the homology is calculated or identified. “extracted” is not a clearly defined or particular step of doing anything with the data provided. “using” the topological filtration is not a positive active method step by which application of a particular algorithm or filter is applied to a particular set of information to achieve a particular goal.
The metes and bounds of claim 8 are unclear. The range appears to lack any sort of units, or modifiers.
The metes and bounds of claim 9 are unclear. The claim fails to particularly point out how the Betti number is to be “based on” the number of rings. This is not a particular direction to make a certain calculation. Further, the term “proteins nodes” in line 2 appears to be a typographical error. Either it should be “protein nodes” or “protein’s nodes” depending on the intent.
The metes and bounds of claims 12-13 are unclear. A statement that a processor or media is configured to do something is not a positive active limitation that the step is actually performed, merely that it could do it.
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 1-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more.
The instant rejection reflects the framework as outlined in the MPEP at 2106.04:
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture, or composition of matter;
(2A) Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
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
(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:
With respect to step (1): yes, the claims are directed to a method/system/NTCRM for therapeutic targeting based on thermodynamic changes in the energy landscape of a protein-protein interaction (PPI) network, the answer is "yes".
With respect to step (2A)(1), the claims recite abstract ideas. To determine if the claims recite any concepts that equate to an abstract idea, law of nature, or natural phenomenon, MPEP at 2106.03 teaches abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships, and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (see MPEP 2106.04(a)(2)). In the instant application, the claims recite the following limitations that equate to an abstract idea with mental steps and mathematical concepts.
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information) (MPEP 2106.04(a)(2). Laws of nature or natural phenomena include naturally occurring principles/ relations and nature-based products that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP2106(b)). Claims 1, 12 and 14 are independent, and all recite nearly identical limitations. Primarily claim 1 is referred to here for clarity. The claims directing to judicial exceptions are as follows:
Abstract ideas: Mathematical concepts
Claims 1, 12, and 14: computing…a thermodynamic measure for each protein node… generating an energy landscape data…generating a PPI subnetwork by applying a topological filtration (filtering data using a calculation related to protein topology)… computing a first Betti number for the PPI subnetwork…sequentially removing a first protein node (data subtraction)… computing a second Betti number… computing a change between the first Betti number and the second Betti number… replacing the first node…sequentially removing a second protein node… computing a third Betti number… computing a change between the first Betti number and the third Betti number… determining…a most significant protein target…
Claim 6: wherein thermodynamic measure is Gibbs free energy for each of the protein nodes within the PPI data is computed using the transcription data and an equation of:.. and an overall Gibbs free energy of all of the protein nodes within the PPI data is computed using an equation of:..
Claim 7: wherein the PPI subnetwork is a persistent homology that is extracted from the energy landscape of the PPI data using the topological filtration based on a user set threshold.
Claim 8: wherein the user set threshold is between 5 to 7000.
Claim 9: wherein the Betti number of the PPI subnetwork is computed based on the number of rings of four or more proteins nodes within the PPI subnetwork.
Claim 11: wherein the change in the Betti number represents an effect that the single protein node has on a network complexity of the PPI data and the single removed protein node that causes a highest drop of the network complexity is the most significant protein target.
Natural phenomenon:
Claims 1, 12, and 14: thermodynamic measure is Gibbs free energy for each of the protein nodes within the PPI data,… transforming and rescaling the transcription data … generating an energy landscape data corresponding to the network of protein nodes …representing persistent homology… wherein an increase in the filtration threshold results in an increase in complexity of the PPI subnetwork…
Claim 7: wherein the PPI subnetwork is a persistent homology that is extracted from the energy landscape of the PPI data using the topological filtration based on a user set threshold.
The claims take transcriptional or genomic data, in combination with thermodynamic energy measures, to identify a “suitable” or “most significant protein” target. This is a correlation between naturally occurring genotype information, naturally occurring aspects of protein structure, and a phenotype of most changed/most significant. This is a naturally occurring correlation.
Hence, the claims explicitly recite elements that, individually and in combination, constitute abstract ideas.
Mathematical concepts recited in claim 1 include:
“computing…a thermodynamic measure for each protein node…” (mathematical concept, a calculation)
“generating an energy landscape data…” (mathematical concept of a mathematical calculation or set of calculations)
“generating a PPI subnetwork by applying a topological filtration…” (mathematical concept of filtering data using a calculation related to protein topology)
“computing a first Betti number for the PPI subnetwork” (mathematical concept, mathematical calculation)
“sequentially removing a first protein node…” (mathematical relationship, subtracting data)
“computing a second Betti number…” (mathematical calculation)
“computing a change between the first Betti number and the second Betti number” (mathematical relationship)
“replacing the first node…sequentially removing a second protein node…” (mathematical relationships of adding or subtracting data)
“computing a third Betti number…” (mathematical calculation)
“computing a change between the first Betti number and the third Betti number” (mathematical calculation)
“determining…a most significant protein target” (calculation, mathematical relationship).
The following limitations in claim 1 claiming a law of nature include:
The claims take transcriptional or genomic data, in combination with thermodynamic energy measures, to identify a “suitable” or most significant protein target. This is a correlation between naturally occurring genotype information, naturally occurring aspects of protein structure, and a phenotype of most changed/ most significant. This is a naturally occurring correlation.
Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas.
With respect to step 2A(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the following additional elements considered for practical application:
Claims 1, 12, and 14: accessing genomic information and PPI data... network of protein nodes from at least one source…
Claim 2: displaying the most significant protein target to a user..
Claim 3: storing, in a data repository, the genomic information and the PPI data.…
Claim 4: an academic database, a public database, and a private database…
Claim 5: genomic information is at least one transcription data selected from a group consisting of messenger RNA (mRNA), RNA sequencing (RNA-seq), and Clustered regularly interspaced short palindromic repeats (CRISPR).
Claim 10: wherein the Betti numbers and respective removed protein nodes are stored in an array.
Claims 12, 14, and 15: processor circuitry, a display circuitry, a display circuitry, or non-transitory computer-readable medium.
Claims 1, 12, 14, and 15 do not utilize the most significant identified protein in any real world or practical application.
Claim 1 recites the additional element that is not an abstract idea: accessing genomic information and PPI data, which is a data gathering step.
Claim 10 recites further data handling: wherein the Betti numbers and respective removed protein nodes are stored in an array.
Data gathering steps are not an abstract idea, they are extra-solution activity, as they collect the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application. (MPEP 2106.05(g).
Claims 12, 14, and 15 also recite the additional non-abstract elements: processor circuitry, a display circuitry, a display circuitry, or non-transitory computer-readable medium. The claims do not describe any specific computational steps by which the computer or system related parts perform or carry out the abstract idea, 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 require nothing more than a generic computer to perform the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not recite integrate that abstract idea into a practical application. (see MPEP 2106.05(f)).
Claim 1, 12, 14, and 15 recite no additional limitation related to the natural law. The claim does not provide a particular limitation which would integrate the natural law into a practical application. To integrate a judicial exception into a practical application, the additional limitation must be specifically identified, and not merely instructions to apply the judicial exception. The additional limitation must have more than a nominal or insignificant relationship to the identified judicial exception. (MPEP 2106.04(d)(2))
Dependent claims 2-11, 13, 15 have been analyzed. Dependent claims 6-11 are directed to further abstract limitations. Further abstract limitations cannot provide a practical application of the judicial exception as they are a part of that exception. Dependent claims 4-5 are directed to additional steps of data gathering. Steps of data gathering do not provide a practical application for the judicial exception. Dependent claims 2-3 are directed to additional computer limitations. These further limitations are still generically stated, and require no more than a standard computer to perform them.
None of these dependent claims recite additional elements which would integrate a judicial exception into a practical application.
Finally, the (2B) analysis. Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims lack a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering, instructions, and field of use limitations described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represent well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either 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 recitations, the claims recite the following additional elements considered for inventive concept:
Claims 1, 12, and 14: accessing genomic information and PPI data... network of protein nodes from at least one source…
Claim 2: displaying the most significant protein target to a user..
Claim 3: storing, in a data repository, the genomic information and the PPI data.…
Claim 4: an academic database, a public database, and a private database…
Claim 5: genomic information is at least one transcription data selected from a group consisting of messenger RNA (mRNA), RNA sequencing (RNA-seq), and Clustered regularly interspaced short palindromic repeats (CRISPR).
Claim 10: wherein the Betti numbers and respective removed protein nodes are stored in an array.
Claims 12, 14, and 15: processor circuitry, a display circuitry, a display circuitry, or non-transitory computer-readable medium.
Said steps that are “in addition” to the recited judicial exception in the instant claims represent those of mere data handling instructions or field of use limitations (data, processing/displaying circuitry, computing system, data repository) to implement in the recited judicial exception and do not impart meaning to said recited judicial exception, such that is applied in a practical manner. Further with respect to the additional elements in the instant claims, these steps direct to mere data gathering and handling (accessing…displaying) to carry out the abstract idea without imposing any meaningful limitation on the abstract idea. Thereby these steps are insignificant extra-solutions activity steps and are insufficient to integrate an abstract idea into a practical application. (MPEP 2106.05(g).
With respect to claim 1: The additional element of data gathering does not rise to the level of significantly more than the judicial exception. Steps of “accessing” genomic information and PPI information are merely steps of accessing data from unspecified databases. The prior art Singh et al. US 2007/0134662 A1 discloses that databases comprising genomic information and PPI information were well known in the art, beginning at paragraph [0088] including BIND, INTERACT, DIP, Pronet-Online, SCOP, PRESAGE et al. All of these databases provide information which could be used to calculate a “thermodynamic measure” which could include free energy, or Gibbs energy (Claim 6)y. Therefore, accessing these databases is considered routine, well understood and conventional in the art. The specification also notes that databases such as TCGA, GEO, and SEER were publicly available or widely used at [0030-0031, 0036]. Activities such as data gathering do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not effect a transformation of matter, nor do they provide a non-conventional or unconventional step. Data gathering steps 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 12-15:the computer related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The prior art Weinan et al. (2013) provides computers which comprise processors, circuits and computer-readable memory for analyzing complex networks such as protein networks. Singh et al (US 2007/0134662 A1) also provides computers and systems comprising the same elements for protein analysis. As such the prior art recognizes that these computing elements are routine, well understood and conventional in the art. The specification also notes that “any combination of mobile, desktop, server, router, switch, embedded device or other types may be used” [0068] in reference to a computer system. 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 an abstract idea (see MPEP 2106.05(b)I-III).
With respect to claims 1, 12, and 14: the additional limitations to the law of nature do not rise to the level of significantly more than the judicial exception. The additional limitations have all been shown to be routine, well-understood and conventional in the art. These limitations in addition to the law of nature do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not effect a transformation of matter, nor do they provide a non-conventional or unconventional step. These additional limitations 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 (MPEP 2106.05(b)&(c).)
Dependent claims 2-11, 13, 15 have been analyzed with respect to step 2B. Dependent claims 4-5 relate to the data gathering discussed above. Dependent claims 2-3 relate to additional computer components discussed above. Dependent claims 6-11 provide further abstract limitations. None of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception.
For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter (Step 2B: No). As such, claims 1-15 are not patent eligible.
Claim Rejections - 35 USC § 103
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. 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 § 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.
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.
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.
Claim 1-4, and 6-15 are rejected under 35 U.S.C. 103 as being unpatentable over Singh (2010) in view of Weinan (2013).
Singh R et al. Struct2Net: a web service to predict protein-protein interactions using a structure based approach. (2010) Nucleic acids research, vol 38, W509. PTO 892 cited; herein Singh.
Weinan E et al. The Landscape of complex networks- critical nodes and a hierarchical decomposition. (2013) Methods and applications of analysis, vol 20 no 4 p 383-404. PTO 892 cited; herein Weinan.
Note: citations from the instant application are italicized in the following section.
The independent claims are drawn to methods (as well as systems, and computer program products) of identifying a significant protein target in a subnetwork of a protein-protein interaction network. The claims access genomic data, and PPI network data, compute a thermodynamic measure for each protein node within the PPI network, generate energy landscape data, and then generate a PPI subnetwork by applying a topological filtration. Once a subnetwork is identified or generated, the subnetwork is analyzed by calculations of the Betti numbers for the subnetwork, sequentially removing nodes of the subnetwork, to identify a node (representing a protein) which when lacking, provokes the greatest change in the Betti number for that subnetwork.
Singh et al provide the overall computer system and program. Singh provides means for accessing genomic and protein-protein interaction data, from various databases including BioGrid, PDB, MINT and/or APID (Methods overview, W510-511). The thermostability of a structure of each protein is calculated and assigned to the node. Protein-protein interactions are calculated on a pair-wise basis. These are used to generate an initial PPI network, based on the likelihood that the structures of the node and its neighbor could structurally interact. (“We compute various energy scores that evaluate the structure (e.g. the quality of the interfacial region, the quality of fit for the individual proteins). Given these, we use logistic regression to predict whether an interaction will occur.”) This is equivalent to the “energy landscape data” of claim 1. Additional parameters are calculated for the model landscape including: interaction terms, non-linear functions of the energy scores, as well as normalized scores. The computer programs, and systems of Singh comprise programmed processors, display aspects, database aspects, and data storage aspects (throughout).
Singh does not specifically address how to identify a subnetwork, or how to identify a node in the subnetwork which may be most significant.
In the field of complex network analysis, Weinan discusses how to identify critical nodes in a network or subnetwork, through the analysis of the topological landscape of a complex network. Weinan introduces the notion that critical nodes representing functions in a network and the connectivity is based on the gradient flow of these functions (abstract). Weinan then defines a concise topological landscape of functions on networks, including a protein-ligand network, a type of PPI (abstract).
Morse acts on the energy landscape data, such as the data provided by Singh (energy scores that evaluate the structures of each protein). Given an energy function on a network, a discrete gradient flow is defined for that function as well as minimum energy paths between two disjoint sets of nodes. This allows the identification of critical nodes or saddles in a network or subnetwork (p384, last full paragraph). This approach provides “a hierarchical composition of networks into hypergraphs with hypernodes as attraction basins of critical nodes, a concise global visualization of networks adaptive to the landscape of a given function.” This allows selection of a subgraph or a subnetwork for further analysis.
In a selected network, subnetwork or subgraph, Weinan then works to identify critical nodes using “persistent homology” (section 2, p 388+). As defined by Weinan, “Persistent homology… is an algebraic tool for computing the Betti numbers and homology groups of a simplicial complex when its faces are added sequentially” (p388). Betti numbers are calculated in an iterative process, removing a node, recalculating the number- replacing that node and removing another, recalculating the Betti number, etc. The most critical or most significant node has the highest degree of change in the compared Betti numbers (Section 2). The Examples (section 3) illustrate the process of identification of the critical or most significant node. One of the Examples (Example 3.3) is one related to protein-protein interactions, structural stability, and molecular dynamics. The free energy calculation is applied to each structural formation and interaction in the network. The free energy landscape is analyzed, with certain subnetworks being identified, and critical nodes within those networks are further identified (Fig 5, Section 3.3). These critical nodes are identified as protein structures which may represent a good target for pharmaceutical intervention to disrupt binding between a protein and its normal ligand.
In KSR Int 'l v. Teleflex, the Supreme Court, in rejecting the rigid application of the teaching, suggestion, and motivation test by the Federal Circuit, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Singh teaches the overall methods for defining energy landscapes of protein-protein interaction networks; however, Singh does not teach identifying proteins of interest by calculation of Betti numbers of subnetworks. However, the identification of nodes of interest (representing a protein target) in a complex network through the calculations of those Betti numbers is a well-known process disclosed by Weinan. Weinan takes a free energy landscape of protein-protein interaction data networks (PPI) and identifies critical subnetworks, comprising a critical node in that subnetwork as having the greatest change in Betti number. The critical node is implicated as a useful target for further study and drug design by Weinan. One of ordinary skill in the art could have applied the known "improvement" technique in the same way to the method, computer program and system of Singh and the results would have been predictable to one of ordinary skill in the art. One would have been motivated to apply the calculations of Weinan to appropriately compare nodes from across the landscape of proteins of Singh, not just a single protein, to capture relationships between protein subnetworks and critical protein targets. One would have had a reasonable expectation of success as the same types of energy landscapes from Singh are used in Weinan for the calculations.
Such a combination is merely a "predictable use of prior art elements according to their established functions." KSR Int’l 7, 127 S. Ct. at 1740.
With respect to claims 2, 15, Singh provides display elements.
With respect to claims 3, 13, Singh provides data storage.
With respect to claim 4, both Singh and Weinan provide data from private, public or academic databases.
With respect to claim 6, Gibbs free energy is calculated by Singh, and Weinan.
With respect to claim 7-8, Weinan provides the persistent homology subnetworks, and thresholds.
With respect to claims 9-11, the Betti number computations are all disclosed by Weinan.
Claims 1-15 are rejected under 35 U.S.C. 103 as being unpatentable over Singh (2010) in view of Weinan (2013) as applied to claims 1-4, 6-15 above, further in view of Peng (2014).
Singh, R. et al. Struct2Net: a web service to predict protein-protein interactions using a structure based approach. (2010) Nucleic acids research, vol 38, W509.
Weinan, E. et al. The Landscape of complex networks- critical nodes and a hierarchical decomposition. (2013) Methods and applications of analysis, vol 20 no 4 p 383-404.
Peng, J. RNA-seq and Microarrays analyses reveal global differential transcriptomes of Mesorhizobium huakuii 7653R between bacteroids and free living cells. (2014) PLOSONE vol 9, issue 4 e93626.
Claim 5 specifies that the genomic data is accessed from transcriptional data, including from RNA-seq or CRISPR experiments.
The independent claims are drawn to methods (as well as systems, and computer program products) of identifying a significant protein target in a subnetwork of a protein-protein interaction network. The claims access genomic data, and PPI network data, compute a thermodynamic measure for each protein node within the PPI network, generate energy landscape data, and then generate a PPI subnetwork by applying a topological filtration. Once a subnetwork is identified or generated, the subnetwork is analyzed by calculations of the Betti numbers for the subnetwork, sequentially removing nodes of the subnetwork, to identify a node (representing a protein) which when lacking, provokes the greatest change in the Betti number for that subnetwork.
Singh et al provide the overall computer system and program. Singh provides means for accessing genomic and protein-protein interaction data, from various databases including BioGrid, PDB, MINT and/or APID (Methods overview, W510-511). The thermostability of a structure of each protein is calculated and assigned to the node. Protein-protein interactions are calculated on a pair-wise basis. These are used to generate an initial PPI network, based on the likelihood that the structures of the node and its neighbor could structurally interact. (“We compute various energy scores that evaluate the structure (e.g. the quality of the interfacial region, the quality of fit for the individual proteins). Given these, we use logistic regression to predict whether an interaction will occur.”) This is equivalent to the “energy landscape data” of claim 1. Additional parameters are calculated for the model landscape including: interaction terms, non-linear functions of the energy scores, as well as normalized scores. The computer programs, and systems of Singh comprise programmed processors, display aspects, database aspects, and data storage aspects (throughout).
Singh does not specifically address how to identify a subnetwork, or how to identify a node in the subnetwork which may be most significant.
In the field of complex network analysis, Weinan discusses how to identify critical nodes in a network or subnetwork, through the analysis of the topological landscape of a complex network. Weinan introduces the notion that critical nodes representing functions in a network and the connectivity is based on the gradient flow of these functions (abstract). Weinan then defines a concise topological landscape of functions on networks, including a protein-ligand network, a type of PPI (abstract).
Morse acts on the energy landscape data, such as the data provided by Singh (energy scores that evaluate the structures of each protein). Given an energy function on a network, a discrete gradient flow is defined for that function as well as minimum energy paths between two disjoint sets of nodes. This allows the identification of critical nodes or saddles in a network or subnetwork (p384, last full paragraph). This approach provides “a hierarchical composition of networks into hypergraphs with hypernodes as attraction basins of critical nodes, a concise global visualization of networks adaptive to the landscape of a given function.” This allows selection of a subgraph or a subnetwork for further analysis.
In a selected network, subnetwork or subgraph, Weinan then works to identify critical nodes using “persistent homology” (section 2, p 388+). As defined by Weinan, “Persistent homology… is an algebraic tool for computing the Betti numbers and homology groups of a simplicial complex when its faces are added sequentially” (p388). Betti numbers are calculated in an iterative process, removing a node, recalculating the number- replacing that node and removing another, recalculating the Betti number, etc. The most critical or most significant node has the highest degree of change in the compared Betti numbers (Section 2). The Examples (section 3) illustrate the process of identification of the critical or most significant node. One of the Examples (Example 3.3) is one related to protein-protein interactions, structural stability, and molecular dynamics. The free energy calculation is applied to each structural formation and interaction in the network. The free energy landscape is analyzed, with certain subnetworks being identified, and critical nodes within those networks are further identified (Fig 5, Section 3.3). These critical nodes are identified as protein structures which may represent a good target for pharmaceutical intervention to disrupt binding between a protein and its normal ligand.
Neither Singh nor Weinan specifically speak to use of transcriptional genomic data as a parameter of the created PPI energy landscapes. Singh does suggest adding additional information and parameters to the energy landscape calculations to improve performance or address a particular experimental data set (p511).
In the field of PPI network analysis and the identification of important or target proteins, Peng utilizes transcriptional data from RNA-seq experiments to create PPI with integrated gene expression data, using a program called Cytoscape. The analysis of differentially expressed genes, in combination with the analysis of the PPI subnetworks revealed a subnetwork with function enrichment for nitrogen fixation, and identified several new uncharacterized genes participating in that function.
In KSR Int 'l v. Teleflex, the Supreme Court, in rejecting the rigid application of the teaching, suggestion, and motivation test by the Federal Circuit, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Singh teaches the overall methods for defining energy landscapes of protein-protein interaction networks. Peng discloses the integration of differential gene expression information for organisms under different conditions (RNA-seq data) in the creation and analysis of PPI networks to identify critical subnetworks and new proteins involved in a critical function (nitrogen fixation). Neither Peng nor Singh teaches identifying proteins of interest by calculation of Betti numbers of subnetworks. However, the identification of nodes of interest (representing a protein target) in a complex network through the calculations of those Betti numbers is a well-known process disclosed by Weinan. Weinan takes a free energy landscape of protein-protein interaction data networks (PPI) and identifies critical subnetworks, comprising a critical node in that subnetwork as having the greatest change in Betti number. The critical node is implicated as a useful target for further study and drug design by Weinan. One of ordinary skill in the art could have applied the known "improvement" technique in the same way to the method, computer program and system of Singh and the results would have been predictable to one of ordinary skill in the art. One would have been motivated to apply the calculations of Weinan to appropriately compare nodes from across the landscape of proteins of Singh, not just a single protein, to capture relationships between protein subnetworks and critical protein targets. One would have had a reasonable expectation of success as the same types of energy landscapes from Singh are used in Weinan for the calculations.
Such a combination is merely a "predictable use of prior art elements according to their established functions." KSR Int’l 7, 127 S. Ct. at 1740.
With respect to claims 2, 15, Singh and Peng each provide display elements.
With respect to claims 3, 13, Singh and Peng provide data storage.
With respect to claim 4, Singh, Peng and Weinan provide data from private, public or academic databases.
With respect to claim 5, RNA-seq data is provided by Peng.
With respect to claim 6, Gibbs free energy is calculated by Singh, and Weinan.
With respect to claim 7-8, Weinan provides the persistent homology subnetworks, and thresholds.
With respect to claims 9-11, the Betti number computations are all disclosed by Weinan.
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.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
A. Instant claims 1-15 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6, 9-10, and 12-15 of US 11,515,004 (07/12/2021). Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are generic to ‘004. US Patent ‘004 is a species of the instant application which is also method to select a protein target for therapeutic application based on genomic information, protein-protein interaction (PPI) data, and thermodynamic measures within a network of protein nodes and a subnetwork with topological filtration.
Relevant Prior Art:
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Benzekry, S. et al. Design principles for cancer therapy guided by changes in complexity of protein-protein interaction networks. (2015) Biology Direct, volume 10, 32. Published after the priority date, this appears to be Applicant’s own work, with two inventors in common.
Gnabasik, D. et al. Discrete time evolution of proteomic biomarkers. (2014) IEEE 2014 Int Conference on Computational Science and Computational Intelligence. Page 11-17. This paper discloses the used of expressed protein information (cytokines) from samples from patients having various lung diseases (cancer, COPD, or nonsmokers) in the creation of PPI networks, to identify the most relevant protein/ cytokine profile for each condition. Gnabasik calculates Betti numbers in the computations of the topological connectedness of the network nodes.
Merelli, E. Topology driven modeling: the IS metaphor. (2015, published online 24 June 2014) Nature Computing, vol 14 p421-430. Merelli computes Betti numbers in the description of the topology of an immune system network.
Emmett, K. Applying topological principles to genomic analysis. (October, 2015) Microbe volume 10 number 11 p467-474. Applying persistent homology analysis to genomic data enables identification of phylogenetic information.
Conclusion
No claims are allowed.
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/VR/
Examiner
Art Unit 1685
/MARY K ZEMAN/Primary Examiner, Art Unit 1686
Prosecution Insights