DETAILED ACTION
Notice of AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon and the rationale supporting the rejection, would be the same under either status.
Status of the Claims
Claims 1-20 are pending.
Claims 1-2, 9-11 and 19-20 are objected to.
Claims 1-20 are rejected.
Priority
This US Application 17/849,653 (06/26/2022) claims no priority herein, as reflected in the filing receipt mailed on 07/08/2022. The claims to the benefit of priority are acknowledged; and the effective filing date of claims 1-20 is 06/26/2022.
Information Disclosure Statement
No Information Disclosure Statement has been filed herein.
Claim Objections
Claims 1-2, 9-11 and 19-20 are objected to because of the following informalities. Appropriate correction is required:
In claims 1, 10 and 19, there is a duplicate enumeration "(ii)" in the first set which should read (i-iii).
In claims 2, 11 and 20, the recited "Asian population" is missing a grammatical article and should read "an Asian population."
In claim 9, the recited "variants … is used …" should read "variants … are used …" for proper subject-verb agreement.
Drawings
The drawings are objected to as failing to comply with 37 CPR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: Public Databases 106 in FIG. 1. Corrected drawing sheets in compliance with 37 CPR 1.12l(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as "amended." If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either "Replacement Sheet" or "New Sheet" pursuant to 3 7 CPR 1.121 ( d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim interpretations
The following claim interpretations apply to all instances of the following terms throughout all claims:
112(f) interpretation of particular recitations
Recited "knowledge extraction engine…" (claim 1)
The above recitation includes means (or an equivalent, nonce term, here "engine") and function and/or result (here "knowledge extraction" interpreted as the function of extracting knowledge). The above recitation is accompanied by sufficient structure in the claims to prevent invoking, i.e. the recited "invoke...," "for each..., analyze..." and "in response... (i)..." Therefore, the recitation is interpreted as not invoking.
Recited "machine learning model" (claims 1, 10 and 19)
Recites means (or an equivalent, nonce term, here "model") and function and/or result (here "machine learning"), but the recitation does not invoke 112/f because it is interpreted as well-known. MPEP 2181.I.A,3rd para. pertains with analogy to structures having "sufficiently definite meaning," such as "filters" and "brakes."
Recited instances of "text mining algorithm" (claims 3 and 12)
Recites means (or an equivalent, nonce term, here "algorithm") and function and/or result (here "text mining"), but the recitation does not invoke 112/f because it is interpreted as well-known. MPEP 2181.I.A,3rd para. pertains with analogy to structures having "sufficiently definite meaning," such as "filters" and "brakes."
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.
Claims 9 and 18 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
Claim 9 recites “construct a chip” which lacks written description under 35 U.S.C. 112(a) as the claim is a system claim that carries out the recited function according to recited structure, and it is not clear that there is both adequate structure recited and adequate disclosure to carry out the recited chip construction, in particularly the recited "system" performance of the recited process steps, i.e. their automation. The specification discloses "the system sends … genetic variants … to a chip designer …" (pg. 11 lines 11-14), however that disclosure is insufficient to support the claimed system physically comprising structure needed for chip fabrication. See MPEP 2163.
Since claim 18, depending from claim 10, is recited as "computer-implemented" (claim 10), then claim 18 is rejected here similarly to claim 9.
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.
Claims 5-6, 8-10, 14 and 17-18 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter of the invention.
The following issues cause the respective claims to be rejected under 112(b) as indefinite:
1. In claim 1, to a "system" interpreted as a 101 machine or manufacture and therefore interpreted according to claimed physical structure, the following "configured to" recitations are unclear as to what is the corresponding physical structure, as required in a machine or manufacture claim:
"engine configured to...,"
"model configured to..." and
"database configured to..."
In each instance, interpretation of the recitation subsequent to the instance is unclear because it is not clear what is the physical structure comprised by the "system" and corresponding to that subsequent recitation. It is not clear what is the physical structure required to be configured as recited. Again, a claim to a machine or manufacture, here a "system," can only be interpreted in terms of its required physical structure, and the physical structure of each of the "engine," "model" and "database" is unclear. The same issues recur in claims 6 and 8. This rejection may be overcome by amending to associated physical structure with the recited instances of "configured to...," for example data or instructions stored in a storage device comprised by the "system." In contrast, in claims 10 and 19, the recited "model" and "database" do not render those claims indefinite because those instances are not recited as "configured to..." and because process steps which are otherwise associated with those instances are properly claimed.
2. Claims 5 and 14 end with a semi-colon, such that it is unclear what is the end of the claim. This rejection may be overcome by ending the claims with a period as required by the MPEP.
3. In claim 6, the second wherein clause does not recite "further" such that its relationship to claim 1 is unclear. It is unclear whether the recitation replaces or adds to claim 1.
4. Claims 9 and 18 recite "construct a chip" which is unclear as to how the chip construction takes place. See 112(a) rejection.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-20 are rejected under 35 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., 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)).
101 background
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two) and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
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)?
Analysis of instant claims
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Regarding claims 1-9, claim 1, in at least some embodiments, requires only unembodied software, which embodiments are not interpreted as belonging to any claim type listed in 101. In a BRI and for at least some embodiments, the claim reads on data and/or software comprising no structure other than data and/or software. The claim is not recited as a process, and the claim is not limited to any particular structure as a 101 machine or manufacture. The claim reads on transitory propagating signals which are not proper patentable subject matter because they do not fit within any of the four statutory categories of invention (In re Nuijten, Federal. Circuit, 2006). Claims 2-9 depend from claim 1 and do not remedy this issue. This issue might be overcome by amending to recite the software or instructions configured according to the recitations of the claims and stored in an element comprised by the claim, e.g. a software storage device comprising instructions configured according to the rest of the claim recitations.
Claims 10-18 are directed to a method, and claims 19-20 are directed to a non-transitory computer storage media storing instructions, each of which falls within one of the categories of statutory subject matter.
[Step 1: claims 1-9 – No; claims 10-20 – 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))?
Background
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)).
Analysis of instant claims
Mathematical concepts recited in instant claims 1, 6, 8, 10, 15, 17 and 19 include the terms:
• "a data crawler to identify research publications" (claims 1, 10 and19);
• "assign/assigning… a score" (claims 1, 6, 8, 10, 15, 17 and 19);
Said terms are being identified as mathematical concepts. 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 having ordinary skill in the art. In this instant disclosure - "logic circuitry" pg. 12-13 - describes the claimed algorithms for identification of data in publications and scoring of data found; which indicates the use of math. Thus, the recited terms corresponds to verbal equivalents of mathematical concepts because they constitute actions executed by a group of mathematical steps in a form of a mathematical algorithm; thus mathematical concepts (MPEP 2106.04(a)(2)). A mathematical concept need not be expressed in mathematical symbols, because "words used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989).
Mental processes, defined as concepts or steps practically performed in the human mind such as steps of observations, evaluations, judgments, analysis, opinions or organizing information include:
"analyze/analyzing content of the research publication" (claims 1, 10 and 19);
• "add/adding the respective genetic variant to a current set" (claims 1, 10 and 19);
• "determine/determining, from the content of the research publication, a phenotype that the respective genetic variant is linked to" (claims 1, 10 and 19);
• "determine/determining one or more characteristics of the research publication" (claims 1, 10 and19);
• "rank/ranking … a score" (claims 1, 10 and 19);
• "extracting, from the text of the research publication, a conclusion with respect to the respective genetic variant" (claims 3 and 12);
• "extracting the second text from the one or more images" (claims 4 and 13); • "extracting, from the content of the research publication, an explanation of a biological reasoning behind the pathogenic genetic variant" (claims 6 and 15);
Under the BRI, the recited limitations are mental processes because a human mind is sufficiently capable of analyze the content of a research publication, organize data by adding a variant to a set, determine a phenotype of the identified variant, identify a characteristic of a publication, rank scores, identify text in a publication text/image, and generate a conclusion/explanation of biological reasoning from data evaluated.
Dependent claims 2 and 20 recite further details about the "particular population" from which the genetic variants are identified; dependent claims 3-4, 6, 12-13 and 15 recite further details about the information extracted from the research publications; dependent claims 5 and 14 recite further details about "characteristics of the research publication" from which the genetic variants are identified; dependent claims 7-9 and 16-18 recite further details about the model (and related parameters) used for genetic variants scoring; not reciting any additional non-abstract elements; all reciting further aspects of the information being analyzed, the manner in which that analysis is performed. Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas. The instant claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). [Step 2A Prong One: claims 1-9 – No at Step 1; claims 10-20 – 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))?
Background
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
Analysis of instant claims
Instant claims 1, 9-10 and 18-19 recite additional elements that are not abstract ideas:
• "store/storing the ranked pathogenic genetic variants" (claims 1, 10 and19) and
• "construct a chip configured to decode human genomes" (claims 9 and 18).
Considerations under Step 2A, Prong Two
The recited limitations regarding data storage are interpreted to require the use of a computer.
The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc .... are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
The recited "store/storing" claims read on receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321 - MPEP 2106.05(a) pertains; which constitutes just necessary data gathering and outputting and therefore correspond to insignificant extra-solution activity. Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)).
The recited limitations regarding "constructing a chip configured to decode genomes" read on a generic "apply it" step because the claim merely recites an idea of a solution or outcome without any indication of how the judicial exception impacts or influences this step yet. There are no additional limitations to indicate details of exactly how the judicial exception is being integrated into the recited step of constructing a chip. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(b).
Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)). None of the dependent claims recite any additional non-abstract elements; they are all directed to further aspects of the information being analyzed, the manner in which that analysis is performed, or the mathematical operations performed on the information.
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements. Additional elements are further discussed in Step 2B below.
Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
At this point in examination it is not yet the case that any of the Step 2A, Prong Two considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of 1. an improvement, 2. treatment, 3. a particular machine or 4. a transformation is clear in the record.
For example, regarding the first consideration at MPEP 2106.04(d)(1), the record, including for example the specification, does not yet clearly disclose a sufficient explanation of improvement over the previous state of the technology field (e.g. pg. 15 lines 10-21). The claims do not yet clearly result in such an improvement.
[Step 2A Prong Two: claims 1-20 - No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
Further, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versa ta Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(Il)(i)).
With respect to claims 1, 10 and 19 and those claims dependent therefrom, the computer-related elements or the general purpose computer and the machine learning model do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (Alice Corp., 573 U.S. at225-26, 110 USPQ2d at 1984; see MPEP 2106.05(A)).
With respect to the instant claims, the prior art review to Castaldo ("Molecular diagnostics: between chips and customized medicine." Clinical Chemistry & Laboratory Medicine 48(7) (2010); newly cited) discloses that scanning a high number of SNPs in large groups of patients and controls using chips can reveal novel susceptibility loci related to complex diseases - pg. 974 col. 1 para. 2; revealing that an additional element which "applies" the judicial exception to a generic computer that is routine, well-understood and conventional in the art.
When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a broad technological environment. See MPEP 2106.05(a) and 2106.05(h). [Step 2B: claims 1-20 - No]
Conclusion: Instant claims are directed to non-statutory subject matter
For these reasons, the claims in this instant application, 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 instant claims 1-20 are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless -
(a)(l) the claimed invention was patented, described in a printed publication, or in public use, on sale,
or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-3, 6-7, 10, 12, 15-16 and 19-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Dong ("iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes." Genome medicine 8(1):135 (2016)), as cited on the attached Form PTO-892.
Dong discloses an integrated cancer genome score (pg. 1 Title) performed by a statistical framework that infers driver variants by integrating contributions from genetic variants to identify cancer driver genes (pg. 1 para. 1). Dong, indicated by the bullet points, teaches the instant features as follows. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims.
Claim 1 discloses:
a. "a system for determining pathogenic genetic variants specific to a particular population, the system comprising: a knowledge extraction engine configured to: invoke, using an application program interface (API), a data crawler to identify research publications related to human genomes of the particular population."
Dong teaches as a program package written in Perl and user interface (i.e. application program interface) written in Ruby on Rails, JavaScript, and HTML5 (pg. 8 col. 1 para. 3), wherein the testing dataset included a The Cancer Genome Atlas data portal web crawler (i.e. knowledge extraction engine/ data crawler) to obtain single nucleotide variants and indels (pg. 4 col. 1 para. 2); wherein testing data comprised admixed Americans, Europeans, Asians, and African populations (i.e. human genomes of the particular population) (pg. 3 col. 2 para. 1).
b. "wherein each of the plurality of research publications refers to a respective genetic variant of a plurality of genetic variants, for each of the plurality of research publications"
Dong teaches as a personalized analysis of mutation data (i.e. plurality of genetic variants) for two patients downloaded from the original publications from Imielinski et al. and Wagle et al. (i.e. plurality of research publications) (pg. 4 col. 1 para. 1).
c. "analyze content of the research publication to determine whether the respective genetic variant is classified as a pathogenic genetic variant according to the research publication"
Dong teaches as modeling the patterns of putative cancer drivers observed in The Cancer Genome Atlas data with a logistic regression model and outputs a prioritized list of genes ranked by their cancer driving potential (pg. 10 col. 1 para. 1).
d. "in response to determining that the respective genetic variant is classified as the pathogenic genetic variant,
(i) add the respective genetic variant to a current set of pathogenic genetic variants,
(ii) determine, from the content of the research publication, a phenotype that the respective genetic variant is linked to, and
(ii) determine one or more characteristics of the research publication"
Dong teaches as a systematic prediction of cancer genetic drivers where a first layer identifies coding mutations, non-coding mutations, and structural variations, and a second layer links these mutation features to genes using a statistical model with prior biological knowledge on cancer driver genes for specific subtypes of cancer (i.e. (ii) determine a phenotype with respect to genetic variant) (pg. 2 col. 2 para. 2); wherein the prior biological knowledge originates from various publicly available databases (pg. 12 col. 1 para. 1); wherein the database mining tool is applied to quantify prior knowledge generated from decades of cancer genetic and its associated genes (i.e. (ii) determine one or more characteristics of the research publication) (pg. 12 col. 1 para. 1); wherein the algorithm output can be accessed via output files (i.e. (i) add the respective genetic variant to a current set of pathogenic genetic variants) (pg. 9 Table 2).
e. " a machine learning model configured to: for each pathogenic genetic variant in the current set of pathogenic genetic variants, assign a respective importance score to the pathogenic genetic variant based on characteristics of research publications from which the pathogenic genetic variant is determined"
Dong teaches as integrating multiple scoring methods to enhance the accuracy of classifying Mendelian disease variants (i.e. assign a respective importance score to the pathogenic genetic variant) which included radial support vector machine learning models that learned the patterns of cancer drivers from a set of confident and experimentally confirmed driver and passenger missense mutations to broadly prioritize cancer genetic drivers for both recurrent and rare mutations (i.e. based on characteristics of research publications from which the pathogenic genetic variant is determined) (pg. 18 col. 1 para. 1).
f. " wherein the respective importance score represents
(i) a level of importance of the pathogenic genetic variant to the particular population and
(ii) a level of contribution of the pathogenic genetic variant to the phenotype that the pathogenic genetic variant is linked to, and rank the pathogenic genetic variants in the current set according to the respective importance scores; and a variant database configured to store the ranked pathogenic genetic variants"
Dong teaches as outputting ranked list of candidate genes based on their association with specific subtypes of cancer (i.e. respective score/level of contribution to a phenotype) (pg. 12 col. 1 para. 1); wherein testing data comprised admixed Americans, Europeans, Asians, and African populations (pg. 3 col. 2 para. 1); wherein the algorithm output can be accessed via output files (i.e. stored in a database) (pg. 9 Table 2)
Claims 10 and 19 are machine or manufacture claims similar to claim 1, and the art is applied to them as described for claim 1 above. Regarding the specific "system" and "media" recitations of claims 10 and 19, Dong teaches a program package written in Perl and user interface (i.e. application program interface) written in Ruby on Rails, JavaScript, and HTML5 (pg. 8 col. 1 para. 3).
Dependent claims 2, 11 and 20 recite "wherein the particular population is Asian population" which Dong teaches as the testing data comprising admixed Americans, Europeans, Asians, and African populations (pg. 3 col. 2 para. 1).
Dependent claims 3 and 12 recite "wherein the content of each research publication includes text, and wherein for each research publication, analyzing the content of the research publication to determine whether the respective genetic variant is classified as the pathogenic genetic variant comprises: extracting, from the text of the research publication, a conclusion with respect to the respective genetic variant by using a text mining algorithm; and determining whether the conclusion classifies the respective genetic variant as the pathogenic genetic variant" which Dong teaches Phenolyzer, a database-mining tool, to utilize valuable prior biological knowledge generated from numerous research studies on cancer and integrate databases on gene–gene and gene–phenotype interaction networks to the model (pg. 19 col. 1 para. 2); and to output a ranked list of candidate genes based on their association with specific subtypes of cancer (i.e. conclusion that classifies the respective genetic variant) (pg. 12 col. 1 para. 1).
Dependent claims 6 and 15 recite "wherein the knowledge extraction engine is further configured to: for each of the plurality of research publications, in response to determining that the respective genetic variant is classified as the pathogenic genetic variant: extracting, from the content of the research publication, an explanation of a biological reasoning behind the pathogenic genetic variant; and wherein the machine learning model is configured to: for each pathogenic genetic variant in the current set of pathogenic genetic variants, assign a respective importance score to the pathogenic genetic variant based on characteristics of research publications from which the pathogenic genetic variant is determined and based on the explanation of the biological reasoning behind the pathogenic genetic variant" which Dong teaches Phenolyzer, database-mining tool, applied to quantify prior knowledge generated from decades of cancer genetic and its associated genes (i.e. determine characteristics of research publications from which the pathogenic genetic variant is determined) (pg. 12 col. 1 para. 1) and integrate databases on gene–gene and gene–phenotype interaction networks to the model (i.e. extracting, from the content of the research publication) (pg. 19 col. 1 para. 2); and to output a ranked list of candidate genes based on their association with specific subtypes of cancer (i.e. explanation of the biological reasoning behind the pathogenic genetic variant) (pg. 12 col. 1 para. 1).
Dependent claims 7 and 16 recite "wherein the machine learning model has one or more parameters, wherein the one or more parameters include one or more of (i) a first parameter representing a clinical effect, (ii) a second parameter representing a number of validations of a research study, (iii) a third parameter representing a size of the research study, (iv) a fourth parameter representing at least one of a p-value, a z-score, or a confidence interval, (v) a fifth parameter representing a variant prevalence, or (vi) a sixth parameter representing metadata of the research study" which Dong teaches the radial support vector machine model being selected to model the patterns of cancer driver mutations, with its parameters further tuned to enhance its performance (i.e. parameter representing a variant prevalence) (pg. 6 col. 1 para. 1).
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 pre-AIA 35 U.S.C. 103(a) 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
A. Claims 4 and 13 are rejected under 35 U.S.C. 103(a) as being unpatentable over Dong as applied to claims 1 and 10 in the 102 rejection above and further in view of Baltoumas ("OnTheFly2. 0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis." NAR Genomics and Bioinformatics 3(4) (2021)), as cited on the attached Form PTO-892.
Regarding claims 4 and 13, Dong teaches the system of claim 1 and method of claim 10 as described above. Claims 4 and 13 further adds "wherein the content of each research publication includes one or more images, the one or more images including second text, and wherein for each research publication, analyzing the content of the research publication to determine whether the respective genetic variant is classified as the pathogenic genetic variant comprises: extracting the second text from the one or more images using optical character recognition; and determining whether the second text classifies the respective genetic variant as the pathogenic genetic variant" which Dong does not teach.
However, Baltoumas teaches a web application for extracting biomedical entities from individual files such as plain texts, office documents, PDF files or images (pg. 1 col. 1 para. 1) using the extract tagging service to perform named entity recognition for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and gene ontology terms (pg. 1 col. 1 para. 1); wherein the application can utilize optical character recognition to produce PDF files with parseable text (pg. 3 col. 1 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 4 and 13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Dong in view of Baltoumas because both references disclose methods for identifying genetic variants. The motivation would have been to detect genes/proteins, genetic variants, and diseases mentioned in documents using a known method as taught by Baltoumas (pg. 2, col. 1, para. 2). Therefore, it would have been obvious to one of ordinary skill in the art to substitute the pathogenic genetic variants identification method of Dong with the pathogenic genetic variants identification method of Baltoumas because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for applying text-mining tools for detection of genetic variants.
B. Claims 5 and 14 are rejected under 35 U.S.C. 103(a) as being unpatentable over Dong as applied to claims 1 and 10 in the 102 rejection above and further in view of Böschen ("Evaluation of JATS decoder as an automated text extraction tool for statistical results in scientific reports" Scientific Reports 11(1):19525 (2021)), as cited on the attached Form PTO-892.
Regarding claims 5 and 14, Dong teaches the system of claim 1 and method of claim 10 as described above. Claims 5 and 14 further adds "wherein the one or more characteristics of the research publication include one or more of: (a) a size of a research study associated with the research publication; (b) a number of times that the research publication has been cited by other publications or other data sources; (c) a p-value that represents quality of test results derived by the research study; or (d) a confidence interval of research findings described in the research publication" which Dong does not teach.
However, Böschen teaches the automated text extraction tool JATSdecoder that extracts all reported statistical results from text (pg. 1 para. 1) and allow an estimation of the sample size which a study is based on (pg. 11 para. 9); wherein a statistical test results mostly consist of a varying set of results (test statistic, degree/s of freedom, an effect measure, p value, confidence interval and/or a Bayes Factor) (pg. 2 para. 7)
Rationale for combining (MPEP §2142-2143)
Regarding claims 5 and 14, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Dong in view of Böschen because both references disclose methods for identifying genetic variants. The motivation would have been, with a little additive text extraction effort, to detect all investigated variables or effects within a research using a known method as taught by Böschen (pg. 11 para. 9). Therefore, it would have been obvious to one of ordinary skill in the art to substitute the identification of information in the web as in Dong with the method identification of information in the web as in Böschen because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for applying text-mining tools for detection of information from research in the web.
C. Claims 8 and 17 are rejected under 35 U.S.C. 103(a) as being unpatentable over Dong as applied to claims 1 and 10 in the 102 rejection above and further in view of Monteiro ("Advanced Text Mining for Annotation of Genomic Variants. MS thesis. Universidade do Minho – Portugal (2018)), as cited on the attached Form PTO-892.
Regarding claims 8 and 17, Dong teaches the system of claim 1 and method of claim 10 as described above. Claims 8 and 17 further adds "wherein, for each pathogenic genetic variant in the current set of pathogenic genetic variants, the machine learning model is configured to assign the respective importance score to the pathogenic genetic variant using a decision tree induction technique in accordance with the one or more parameters of the machine learning model" which Dong does not teach.
However, Monteiro teaches Text-Mining Machine Learning-based tool that aimed at providing the user with a likelihood of whether such variants are more probable to be ‘Benign’ or ‘Pathogenic’ in a given disease context (pg. 6 para. 1); wherein a tree structure was built by the Decision Tree model for the Frequency Matrix with Disease Score (Fig. 15 pg. 107).
Rationale for combining (MPEP §2142-2143)
Regarding claims 8 and 17, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Dong in view of Monteiro because both references disclose methods for identifying information in the web. The motivation would have been to understand the relation between a variant present in an individual and a certain disease/phenotype using a known method as taught by Monteiro (pg. 2 para. 3). Therefore, it would have been obvious to one of ordinary skill in the art to substitute the pathogenic genetic variants identification method of Dong with the pathogenic genetic variants identification method of Monteiro because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for applying text-mining tools for detection of genetic variants.
C. Claims 9 and 18 are rejected under 35 U.S.C. 103(a) as being unpatentable over Dong as applied to claims 1 and 10 in the 102 rejection above and further in view of Castaldo ("Molecular diagnostics: between chips and customized medicine." Clinical Chemistry & Laboratory Medicine 48(7) (2010)), as cited on the attached Form PTO-892.
Regarding claims 9 and 18, Dong teaches the system of claim 1 and method of claim 10 as described above. Claims 9 and 18 further adds "wherein the ranked pathogenic genetic variants stored in the variant database is used to construct a chip configured to decode human genomes of individuals in the particular population" which Dong does not teach.
However, Castaldo teaches scanning a high number of single nucleotide polymorphisms in large groups of patients and controls using chips can reveal novel susceptibility loci related to complex diseases (pg. 974 col. 1 para. 2).
Rationale for combining (MPEP §2142-2143)
Regarding claims 9 and 18, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Dong in view of Castaldo because both references disclose methods for identifying information in the web. The motivation would have been to apply genotyping chip platforms to study nucleic acids in fine detail (pg. 973 col. 2 para. 3) revealing a large number of genetic loci potentially associated with complex diseases (pg. 976 col. 2 para. 4) using a known method as taught by Castaldo. Therefore, it would have been obvious to one of ordinary skill in the art to substitute the pathogenic genetic variants identification method of Dong with the pathogenic genetic variants identification method of Castaldo because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for detection of genetic variants.
Conclusion
No claims are allowed.
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/F.F.L./Examiner, Art Unit 1685
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686