DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 1-22 are pending and examined herein.
No claims are canceled.
Priority
As detailed on the 10 April 2024 filing receipt, the application claims priority as early as 16 March 2021. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Information Disclosure Statement
Information disclosure statement (IDS) was filed on 31 January 2024. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the references are being considered by the examiner.
Specification
The disclosure is objected to because of the following informalities: “by” is duplicated (paragraph [70], line 17), “correlations” is misspelled as “corelations” (paragraph [185]), and “Phylogenomics” is misspelled as “Phylgenomics” (pg. 53, line 24).
Appropriate correction is required.
Claim Objections
Claims 16 and 22 are objected to because of the following informalities: the term “correlation value” is missing an article and should likely read “a correlation value”. 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 the modules recited in claims 1, 16, and 19.
The nonce term “module” is recited as performing functional steps including receiving inputs, generating a first matrix, performing singular value decomposition, quantifying biological information, correlating statistical interactions with benchmarked biological interactions, classifying protein-protein interaction, developing a null model, identifying proteins that are significantly correlated with a protein, determining a spectral depth, identifying networks of proteins, assigning a function, obtaining hierarchical interactions, and characterizing a protein. However, the claims do not recite sufficient structure for said modules.
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.
The specification discloses at least the first five modules (claim 1) may be stored in memory and executed by a processor (paragraphs [214-216]), and so the steps are interpreted as implemented using a general purpose computer. Modules sixth through twelve (claims 16 and 19) are not specifically disclosed to have the structure of a computer processor.
It is noted that claims 21-22 also recite modules carrying out the steps, but these are disclosed as stored in a computer-readable medium executed by processors, and thus are understood as instructions implemented by a computer.
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(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 16-20 are rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, because the claim purports to invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, but fails to recite a combination of elements as required by that statutory provision and thus cannot rely on the specification to provide the structure, material or acts to support the claimed function. Regarding claims 16 and 19, neither the claims nor the disclosure recite or disclose a specific means beyond the modules for the modules’ functions. As such, the claims recite functions that have no limits and cover every conceivable means for achieving the stated functions. Accordingly, the disclosure is not commensurate with the scope of the claim. Claims 17-18 and 20 are similarly rejected because they are dependent on claims 16 and 19, and do not resolve the lack of structure in their parent claims.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
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 16-20 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.
Claims 16 and 19 recite limitations including modules for performing certain steps which invoke 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 as explained in the claim interpretation above. Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. Claims 17-18 and 20 are similarly rejected because they are dependent on claims 16 and 19, and do not resolve the lack of clarity in the parent claims.
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.
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 1-22 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). The claims as a whole, considering all claim elements individually and in combination, are directed to a judicial exception at Step 2A, Prong 2, and the additional elements of the claims, considered individually and in combination, do not provide significantly more at Step 2B than the abstract idea of determining interactions between proteins.
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of
nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to a method (claims 1-20) and a non-transitory computer-readable medium (claims 21-22), each of which falls within one of the categories of statutory subject matter. [Step 1: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Claims 1 and 21 recite generating a matrix of values where the rows correspond to organisms, the columns correspond to genetic elements, and the cells have numbers of occurrences, and thus describe a mathematical concept.
Claims 1 and 21 recite performing singular value decomposition, which is a mathematical concept.
Claims 1 and 21 recite quantifying by pair-wise correlation to obtain statistical interaction, where quantification, pair-wise correlation, and calculation of statistics are all verbal descriptions of mathematical concepts.
Claims 1 and 21 recite correlating statistics with biological interactions. Correlation may be considered a mental step of evaluating information. Correlation may also be considered, given its broadest reasonable interpretation in light of the specification, a mathematical concept as the specification discloses “the correlating step is conducted by quantifying mutual information” where quantification is considered a mathematical step.
Claims 1 and 21 recite classifying an interaction using the correlations, where classification is a step of data evaluation or opinion and thus a mental process.
Claims 2-6 recite the type of data being analyzed. Information or “data per se” is not directed to any statutory category.
Claim 7 recites producing scaling for the matrix showing fractional variance, and is considered further description of the mathematical concept of SVD.
Claim 8 recites further information about the pair-wise correlation, which is then also considered to be directed to abstract ideas.
Claims 9-10 recite data or information being analyzed as part of the correlating step, where the correlating step is previously interpreted as an abstract idea, and information or “data per se” is not directed to any statutory category.
Claim 11 recites classification using random forest models. Random forest models are ensembles of decision trees which are conditional algorithms, which is considered to be a mathematical concept.
Claim 12 recites dividing the matrix, where dividing in the information is a step of data organization and thus a mental process. Claim 12 also recites computing correlations for each genetic element pair, where computing a correlation is interpreted as a mathematical concept.
Claims 13-15 recite information or data analyzed by the random forest model. Information or “data per se” is not directed to any statutory category.
Claim 16 recites developing a null model, where a null model for a mathematical concept is considered to be a mathematical concept, which is supported by the specification (Fig. 16).
Claim 16 recites identifying proteins that are statistically significantly correlated, where significant correlation requires calculation of a statistic and thus is a mathematical concept.
Claim 16 recites determining spectral depth correlation for all pairs of proteins, where determining a correlation is interpreted as a mathematical concept.
Claim 16 recites identifying networks of proteins sharing a depth to obtain statistical modules based on density, where using statistics to determine density is considered to be a mathematical concept.
Claim 16 recites assigning functions using gene enrichment analysis, where assigning a function is a mental step of data evaluation.
Claim 16 recites obtaining hierarchical interactions by comparing functions, where data comparison is a step practically performed by the human mind.
Claims 17-18 recites a where to place the windows and information about the window, where the window placement is a mental step of data selection.
Claim 19 recites characterizing a protein in the model as having the function of the model is a mental step of data evaluation or judgment.
Thus, the claims recite abstract ideas and thus must be examined further to determine whether elements in addition to the abstract ideas integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). [Step 2A Prong One: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Because the claims recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they recite elements in addition to the abstract ideas which integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(III)).
Claims 1 and 21 recite receiving information.
Claims 1, 16, 20, and 21-22 recite displaying information.
Claims 21-22 recite a non-transitory computer-readable storage medium and one or more processors.
Receiving information is a data gathering step required to perform the abstract mental and mathematical steps. Therefore, this step is considered to be insignificant extra-solution activity (MPEP 2106.05(g)). The display steps read on data outputting, which is also insignificant extra-solution activity (MPEP 2106.05(g)). The non-transitory computer readable medium and processor are computer components. There is no specific computational step(s) by which the computer performs or carries out the abstract idea, nor is there any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than that a generic computer performs 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 integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
Thus, the claims recite elements in addition to the abstract ideas which do not integrate the abstract ideas into a practical application, and must be examined further to determine whether elements in addition to the abstract ideas provide significantly more (MPEP 2106.05). [Step 2A Prong Two: Yes]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
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 of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05). The claims recite a computer, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions, which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
Claims 1 and 21 recite receiving information.
Claims 1, 16, 20, and 21-22 recite displaying information.
Claims 21-22 recite a non-transitory computer-readable storage medium and one or more processors.
The courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93 (storing and retrieving information in memory), as discussed in MPEP 2106.05(d)(II)(i)).
Display steps are interpreted as insignificant extra-solution activity (MPEP 2106.05(g)) which do not impose meaningful limits on the claim, here displaying an output of the analysis (Ameranth, 842 F.3d at 1241-42, 120 USPQ2d at 1854-55; MPEP 2106.05(g)).
Therefore, the recited additional elements, alone or in combination, do not appear to provide an inventive concept. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as
being directed to non-statutory subject matter.
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 section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-3, 5-6, 9-10, and 21
Claims 1-3, 5-6, 9-10, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Stuart (BMC Bioinformatics 5(204): 13 pgs., 2004; newly cited) in view of Franceschini (Bioinformatics 32(7): 1085-1087, 2016; previously cited on the 31 January 2024 IDS form) and Moi (Plos Computational Biology 16(7): 21 pgs., 2020; newly cited).
Claim 1 recites receiving, at a first module, inputs corresponding to detectable proteomes of organisms, the inputs derived from sequencing genomes of the organisms.
Stuart teaches analysis of genomes (abstract) and application to proteomes (pg. 10, col. 2, first paragraph).
Claim 1 recites generating, at the first module, a first matrix comprising a plurality of rows and a plurality of columns, where each of the plurality of rows corresponds to a detectable proteome of an organism, and where each of the plurality of columns corresponds to a genetic element, and where an entry in the first matrix represents a number of times each genetic element appears in each detectable proteome.
Stuart teaches recording raw frequencies for the genetic elements in each organism of interest (pg. 12, col. 1, first paragraph).
Claim 1 recites performing, at a second module, singular value decomposition (SVD) on the first matrix to generate a second matrix, where the second matrix is a spectral matrix representing a variation for each genetic element.
Stuart teaches performing singular value decomposition on the above data matrix (pg. 12, col. 1, first paragraph).
Claim 1 recites quantifying, at a third module, biological information contained in one or more cells of the spectral matrix by calculating pair-wise correlations for the genetic elements to obtain statistical interactions between the genetic elements at different scales of variation.
Franceschini teaches calculating pairwise distances between units in the matrix (pg. 1085, col. 2, last paragraph to pg. 1086, col. 1, first paragraph).
Moi teaches relationships at different phylogenetic scales using a hierarchical approach (abstract).
Claim 1 recites correlating, at a fourth module, the obtained statistical interactions with benchmarked biological interactions.
Franceschini teaches benchmarking predicted associations (pg. 1086, col. 1, second paragraph).
Claim 1 recites classifying, at a fifth module, a protein-protein interaction using the correlations between statistical interactions and the benchmarked biological interactions.
Franceschini teaches protein-protein interaction predictions (pg. 1086, col. 2, second and third paragraphs).
Claim 1 recites displaying information indicating the classification to a user.
Franceschini teaches display of interactions (Fig. 1) and interaction degree (pg. 1086, col. 1, fourth paragraph).
Claim 21 recites a non-transitory computer-readable medium storing instructions executed by a processor to perform the steps of claim 1.
Stuart, Franceschini, and Moi teach the steps of claim 1, and Franceschini teaches a program to perform the steps at SVD-Phy (abstract) and thus a computational environment, which would be obvious to a person having ordinary skill in the art.
Claim 2 recites the organisms comprise prokaryotic organisms or eukaryotic organisms.
Stuart teaches application to eukaryotic organisms (abstract).
Claim 3 recites the organisms are prokaryotic organisms.
Franceschini teaches testing their algorithm on prokaryotic organisms (pg. 1086, col. 1, second paragraph).
Claim 5 recites the genetic element includes an orthologous gene group.
Stuart and Franceschini do not require the taught tetrapeptides are orthologous gene groups.
Moi teaches orthologous groups (abstract).
Claim 6 recites the genetic element includes a conserved protein domain.
Stuart teaches comparison of conserved amino acid motifs and gene families (pg. 2, col. 1, first paragraph).
Claim 9 recites the benchmarked biological interactions include phylogenetic relationships, indirect protein interactions in cellular pathways, direct protein interaction, or a mixture of indirect and direct interactions.
Franceschini teaches benchmarking using the KEGG pathway (pg. 1086, col. 1, second paragraph).
Claim 10 recites the correlating step is conducted by quantifying mutual information shared between the statistical interactions and benchmarked biological interactions.
Franceschini teaches quantification as a percent precision and number of interactions (pg. 1086, col. 1, fourth paragraph).
Combining Stuart and Franceschini
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine the works of Stuart and Franceschini because the latter is applied to protein-protein interactions but not at the -omic scale whereas Stuart teaches protein prediction at the genome scale, and more specifically teaches proteome datasets (pg. 2, col. 1, second paragraph) and interpreting proteomic datasets (pg. 10, col. 2, first paragraph). Therefore, the application of the interactions of Franceschini would be prima facie obvious to combine with the -omic scale of Stuart as they are directed to the shared field of endeavor of using singular value decomposition for protein analysis. Further combination with Moi would be advantageous because Moi teaches SVD with respect to orthologous groups, which is a particularly interesting classification in view of organisms’ phylogeny because orthologous arise from a common ancestor and so contain phylogenetic information (pg. 14, fifth paragraph). Stuart, Franceschini, and Moi are all directed to the shared field of endeavor of SVD for genetic analysis and their combination is prima facie obvious.
Claim 4
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Stuart in view of Franceschini and Moi as applied to claims 1-3, 5-6, 9-10, and 21 above and further in view of Marcolino (Genome Visualization in Space, pgs., 225-232, in Advances in Bioinformatics, Springer-Verlag: Berlin, 244 pgs., 2010; newly cited).
Claim 4 recites the organisms are mammalian organisms.
Stuart teaches application to some (but not all) mammalian organisms (Table 1).
Marcolino teaches application of SVD techniques to mammals (abstract).
Combining Stuart, Franceschini, Moi, and Marcolino
Stuart and Franceschini teach application of SVD to eukaryotic organisms (Stuart: abstract), prokaryotic organisms (Franceschini: pg. 1086, col. 1, second paragraph), and a mix including mammals (Stuart: Table 1). Marcolino teaches SVD with respect to mammals (abstract). The SVD technique for genetic analysis across organisms is agnostic to the type of organism being analyzed, and so it is considered a simple substitution to one having ordinary skill in the art to use whatever the organisms of interest are. MPEP 2143(B) pertains.
Claims 11 and 13-14
Claims 11 and 13-14 are rejected under 35 U.S.C. 103 as being unpatentable over Stuart in view of Franceschini and Moi as applied to claims 1-3, 5-6, 9-10, and 21 above and further in view of Ding (International Journal of Molecular Sciences 17(1623): 14 pgs., 2016; newly cited).
Claim 11 recites the classifying is conducted using one or more trained Random Forest models.
Ding teaches using a Random forest for judging interaction pairs and non-interaction pairs of protein-protein interactions (abstract).
Claim 13 recites the one or more trained Random Forest models are trained using orthologous gene groups.
Ding teaches interacting proteins and orthologs in other organisms (pg. 7, first paragraph).
Claim 14 recites the one or more trained Random Forest models are trained using conserved protein domains.
Stuart teaches comparison of conserved amino acid motifs and gene families (pg. 2, col. 1, first paragraph).
Combining Stuart, Franceschini, Moi, and Ding
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine the works of Stuart and Franceschini with Ding because Ding teaches using random forests to classify the interactions. Franceschini at least teaches analysis of the interactions but Ding teaches an improvement in the form of using random forests as having excellent performance in classification tasks (pg. 12, Section 4.5). As Ding is also directed to the shared field of endeavor of protein-protein interaction analysis based on singular value decomposition, combination of Ding with the previously combined work is prima facie obvious.
Claim 15
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Stuart in view of Franceschini, Moi, and Ding as applied to claims 1-3, -56, 9-11, 13-14, and 21 above and further in view of Keseler (Nucleic Acids Research 41: 8 pgs., 2012; newly cited).
Claim 15 recites the Random Forest models are trained using protein interaction information of E. coli K12.
Franceschini teaches benchmarking using E. coli as found in Keseler, where it is in turn taught that E. coli K12 in particular was used as a reference (abstract).
Combining Stuart, Franceschini, Ding, and Keseler
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine Keseler with the previously combined works, particularly that of Franceschini, because Franceschini teaches benchmarking with respect to E. coli as taught by Keseler, and Keseler teaches E. coli K12 (abstract), making their combination obvious. Furthermore, Keseler teaches E. coli K-12 is a good reference genome because it has undergone comparatively minimal genetic manipulation since its isolation (pg. 4, col. 2, last paragraph). Therefore, the combination is considered prima facie
Subject Matter Free of the Prior Art
Claim 7 recites the SVD on the first matrix further produces a scaling for the spectral matrix showing that fractional variance of at least some components is linearly related to a component number, and wherein these components are used in the quantifying step.
Claim 8 recites the pair-wise correlations for the genetic elements are calculated within all five-component windows of the one or more cells of the spectral matrix.
Claim 12 recites the one or more trained Random Forest models are trained via steps of: dividing the spectral matrix obtained from the SVD into two or more mutual information windows, each of which is enriched for information representing at least one biological interaction; and computing spectral correlations for each genetic element pair over each mutual information window.
Claim 16 teaches additional steps related to emergent biological function prediction, network analysis, and enrichment analysis.
While Moi teaches scalable profiling by use of hierarchical orthologous groups (abstract), the prior art is not considered to teach or fairly suggest scaling showing that fractional variance of at least some components is linearly related to a component number (claim 7), pairwise correlation within a set window (claim 8), the specific training steps (claim 12), or additional steps related to emergent biological function prediction, network analysis, and enrichment analysis (claim 16 and its dependents). Therefore, these claims are considered free of the prior art.
Conclusion
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/Robert J. Kallal/Examiner, Art Unit 1685
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