DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Status of claims
Canceled:
none
Pending:
1-17
Withdrawn:
none
Examined:
1-17
Independent:
1, 11 and 17
Allowable:
none
Rejections applied
Abbreviations
x
112/b Indefiniteness
PHOSITA
"a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention"
112/b "Means for"
BRI
Broadest Reasonable Interpretation
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
x
102, 103
JE
Judicial Exception
x
101 JE(s)
112/a
35 USC 112(a) and similarly for 112/b, etc.
101 Other
N:N
page:line
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed on the 8/10/2021 filing receipt, this application claims priority to no earlier than 10/16/2018. All claims have been interpreted as being accorded this priority date.
Citations in the specification are not information disclosure statements
Information Disclosure Statements (IDSs) have been considered as indicated by the accompanying Form 1449 annotated IDS.
The listing or citation of references in the specification does not constitute an IDS (for example: pp. 16-19). 37 CFR 1.98(b) requires a list of patents, publications, or other information submitted for consideration by the office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited on an IDS or by the examiner on form PTO-892, they have not been considered.
Claim objections
Claims 1 and 16 are objected to because of the following informalities. Appropriate correction is required. In each objection the claims are definite with respect to the issues cited here because interpretation would have been sufficiently clear to PHOSITA, but nonetheless the claims are objected to for consistency among the claims or as otherwise indicated. With regard to any suggested amendment below to overcome an objection, in the subsequent examination it is assumed that each amendment is made. However, equivalent amendments also would be acceptable. Any amendments in response to the following objections should be applied throughout the claims, as appropriate.
The following issues are objected to:
Claim
Recitation
Comment
1
one or more specialized architecture
Probably should read "one or more specialized architectures" plural for correspondence with the recited "more"
16
termregularizes
Missing space: "term regularizes"
Claim rejections - 112/b
The following is a quotation of 35 USC 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 1-17 are rejected under 112/b, as indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention. Claims depending from rejected claims are rejected similarly, unless otherwise noted, and any amendments in response to the following rejections should be applied throughout the claims, as appropriate. With regard to any suggested amendment below, for claim interpretation during the present examination it is assumed that each amendment suggested here is made. However equivalent amendments also would be acceptable.
The following issues cause the respective claims to be rejected under 112/b as indefinite:
Claim
Recitation
Comment (suggestions in bold)
1-2, 11, 17
large-scale
The recited "large-scale" is a term of relative or vague degree or form of association, neither defined in the specification (e.g. p. 1, last para. and p. 8, last para.), nor having a well-known and sufficiently particular definition in the art and in the instant context. (MPEP 2173.05(b) pertains.) Although claims are interpreted in light of the specification, examples from the specification are not imported into the claims as limitations, absent a clearly limiting definition in the specification. (MPEP 2145.VI pertains.)
1, 11, 17
specialized
The recited "specialized" is a term of relative or vague degree or form of association, neither defined in the specification (e.g. p. 2, 2nd para.), nor having a well-known and sufficiently particular definition in the art and in the instant context. (MPEP 2173.05(b) pertains.) In claim 11, each instance, i.e. "one or more specialized architecture" and "a specialized architecture memory," renders the claim indefinite. Claim 4 remedies this rejection and is not similarly rejected.
1, 11, 17
highly
The recited "highly" is a term of relative or vague degree or form of association, neither defined in the specification (e.g. p. 9, 2nd para.), nor having a well-known and sufficiently particular definition in the art and in the instant context. It is understood that terms such as "highly" and "massively" parallel occur in computational fields, however it is not clear that a sufficiently clear cut-off exists between such systems and systems which are insufficiently parallelized to be included among such systems, so as to provide a clear scope for instant claims reciting the term "highly." (MPEP 2173.05(b) pertains.)
1, 8-11, 15-17
the specialized architecture
The recitation requires but lacks clear antecedent, there being no clear relationship between this singular instance and the possible plurality in the preceding "one or more specialized architecture."
2-3
bulk
The recited "bulk" is a term of relative or vague degree or form of association, neither defined in the specification (e.g. p. 2, penultimate para.), nor having a well-known and sufficiently particular definition in the art and in the instant context. (MPEP 2173.05(b) pertains.)
2-3, 5, 9
optionally
In the recited context, it is unclear whether the recited "optionally" is an alternative to the preceding recitation or an optional addition.
10, 16
patient/sample signature or cluster memberships
The grammar and/or punctuation is unclear at least because it is unclear which adjectives modify which nouns.
Claim interpretations
The following claim interpretations apply to all instances of the following terms throughout all claims:
Example
Claim
Recitation
Comment
1
central processor unit (CPU) memory
In a BRI, the recited CPU memory reads on any of CPU-internal or CPU-onboard registers, CPU-proximate cache of any level, e.g. 1, 2, 3, 4 including static random access memory (SRAM) or CPU or computer system random access memory (CPU RAM) including any form of dynamic RAM (DRAM). The recited CPU memory does not read on other storage devices such as magnetic hard disk drives, solid state disk drives, magnetic tape drives, network-attached storage, etc.
Claim rejections - 102
In the event the determination of the status of the application as subject to AIA 35 USC 102 and 103 is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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)(1) 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.
Claims 1-2, 4-5, 7, 9, 11-12, 14 and 17
Claims 1-2, 4-5, 7, 9, 11-12, 14 and 17 are rejected under 35 USC 102(a)(1) as anticipated by Zbiljic (US2017/0318119A1 as cited on the 4/12/2021 IDS).
Regarding claim 1, the recited receiving at a computer network node a large biological dataset reads on "...functionality for stream-processing biomedical data" and "...processing large amounts of data, such as sequence reads..." (Zbiljic: [45]; also FIG. 1A-D, network 104; and entire document).
The recited storing in CPU memory reads on "main memory" (Zbiljic: [21]; also FIG. 1A-D, main memory 122; and entire document).
The recited passing data to a specialized architecture reads on "...executing on one or more machines 106 to support a particular analysis (e.g., including multi-threaded or parallel environments)..." (Zbiljic: [126]; also [59, 103]; and entire document) and "Any of the foregoing may be... incorporated in, specially designed ASICs (application-specific integrated circuits) or FPGAs (Field-Programmable Gate Arrays)" (Zbiljic: [131]; and entire document).
The recited genomics analysis reads on "provide pre-fetching for data used in genotyping a small region of the genome across a large sample cohort. ... Analyses such as these can be quite large..." (Zbiljic: [115]; also [3, 127]; and entire document).
The recited outputting reads on "This tool takes a list of FASTQ files as input, accesses and analyzes file metadata, and outputs grouped files according to pairs of paired-end sequence reads" (Zbiljic: [120]; also [129]; and entire document).
Claim 2 narrows to bulk sequence or expression data, which reads on "a file having a text-based format for storing... a biological sequence" (Zbiljic: [43]; also [4, 42, 117]; and entire document).
Claims 4-5 are taught as described above for claim 1.
Claim 7 narrows to the dataset being a count matrix, which reads on "counter matrix" (Zbiljic: [99]; and entire document).
Claim 9 narrows to an algorithm initially designed for CPU computing is executed on specialized architecture, which reads on "Using traditional methods, this would require that each file be downloaded individually onto a computational instance before processing. ... some embodiments of file systems described herein allow a user to analyze thousands of samples simultaneously in one workflow..." (Zbiljic: [116-117]; also [113, 126]; and entire document).
The art is applied to claims 11-12, 14 and 17 as described above for claims 1-2, 4-5, 7 and 9.
Claim rejections - 35 USC 103
In the event the determination of the status of the application as subject to AIA 35 USC 102 and 103 is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 USC 103 which forms the basis for all obviousness rejections set forth in this office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102 of this title, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 USC 102(b)(2)(C) for any potential 35 USC 102(a)(2) prior art against the later invention.
Claim 3
Claim 3 is rejected under 35 USC 103 as unpatentable over Zbiljic in view of Alter (US20140303029A1 as cited on the 4/12/2021 IDS).
The art is applied to claims 1 and 11 as described in the above 102 rejection.
Claim 3 narrows to a biologic dataset from bulk tissue or cells, which reads on "...biological data may be derived from a patient-specific sample including a normal tissue, a disease-related tissue or a culture of a patient’s cell (normal and/or disease-related)" (Alter: [124]; also [3, 38, 116, 290]; and entire document).
Combining Zbiljic and Alter
In the absence of a secondary consideration to the contrary, it would have been prima facie obvious for PHOSITA to modify the large bio data teaching of Zbiljic using the related teaching of Alter. As motivation to combine, an advantage taught by Alter of modifying methods such as those of Zbiljic would have been the teaching of Alter that "In the field of biotechnology, these matrices may represent biological reality through large-scale molecular biological data..." (Alter: [4]). Thus, PHOSITA would have been motivated to modify Zbiljic using the above techniques of Alter in order to achieve the above advantage. One would have had a reasonable expectation of success in doing so because Zbiljic and Alter are generally drawn to related teaching, and PHOSITA would have understood how to and would have been motivated to apply the teaching of Alter to the related teaching of Zbiljic.
Claims 6 and 13
Claims 6 and 13 are rejected under 35 USC 103 as unpatentable over Zbiljic in view of Glynias (US20150073719A1 as cited on the 4/12/2021 IDS).
The art is applied to claims 1 and 11 as described in the above 102 rejection.
Claims 6 and 13 narrow to a variant call format (VCF) dataset, which reads on "variant call format, or VCF" (Glynias: [6]; and entire document).
Claims 8, 12 and 15
Claims 8, 12 and 15 are rejected under 35 USC 103 as unpatentable over Zbiljic in view of Mueller (US20100216653A as cited on the 4/12/2021 IDS).
The art is applied to claims 1 and 11 as described in the above 102 rejection.
Claims 8 and 15 narrow to particular recited operations, which read on "The p-values were obtained in the analysis of MPI sample, using Armitage trend test with... covariates..." (Mueller: [53]; also [4-5, 66-67]; and entire document).
Claim 12 narrows analysis type to GWAS, QTL or Bayesian matrix factorization, at least one of which reads on "Genome-wide association (GWA) scans" (Mueller: [4-5]; and entire document).
Combining Zbiljic and Mueller
In the absence of a secondary consideration to the contrary, it would have been prima facie obvious for PHOSITA to modify the large bio data teaching of Zbiljic using the related teaching of Mueller. Applying the statistical techniques of Mueller to Zbiljic would have been an example of combining prior art elements according to known methods to yield predictable results and use of a known technique to improve similar methods. Thus, PHOSITA would have been motivated to modify Zbiljic using the above techniques of Mueller in order to achieve the above advantage. One would have had a reasonable expectation of success in doing so because Zbiljic and Mueller are generally drawn to related teaching, and PHOSITA would have understood how to and would have been motivated to apply the teaching of Mueller to the related teaching of Zbiljic.
Claims 10 and 16
Claims 10 and 16 are rejected under 35 USC 103 as unpatentable over Zbiljic in view of Loring (US20110118130A1 as cited on the 4/12/2021 IDS).
The art is applied to claims 1 and 11 as described in the above 102 rejection.
Claims 10 and 16 narrow to Non-negative Matrix Factorization and W and H matrices and lambda term computations, which read on "NMF computes two component matrices, the W matrix... and the H matrix..." (Loring: [270]; [183-185, 265, 271, 276]; and entire document).
Combining Zbiljic and Loring
In the absence of a secondary consideration to the contrary, it would have been prima facie obvious for PHOSITA to modify the large bio data teaching of Zbiljic using the related teaching of Loring. Applying the statistical techniques of Loring to Zbiljic would have been an example of combining prior art elements according to known methods to yield predictable results and use of a known technique to improve similar methods. Thus, PHOSITA would have been motivated to modify Zbiljic using the above techniques of Loring in order to achieve the above advantage. One would have had a reasonable expectation of success in doing so because Zbiljic and Loring are generally drawn to related teaching, and PHOSITA would have understood how to and would have been motivated to apply the teaching of Loring to the related teaching of Zbiljic.
Claim rejections - 101
35 USC 101 reads:
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.
For each rejection below, dependent claims are rejected similarly as not remedying the rejection, unless otherwise noted.
Judicial exceptions (JE) to 101 patentability
Claims 1-17 are rejected under 35 USC 101 because the claimed inventions are not directed to patent eligible subject matter. After consideration of relevant factors with respect to each claim as a whole, each claim is directed to one or more JEs (i.e. an abstract idea, a natural phenomenon, a law of nature and/or a product of nature), as identified below. Any elements or combination of elements beyond the JE(s) (i.e. "additional elements") are conventional and do not constitute significantly more than the JE(s). Thus, no claim includes additional elements amounting to significantly more than the JE(s), as explained below.
In Alice, citing Mayo and Bilski, two Mayo/Alice questions determine eligibility under 101: First, is a claim directed to a JE? And second, if so, does the claim recite significantly more than the JE?
MPEP 2106 organizes JE analysis into Steps 1, 2A (1st & 2nd prongs) and 2B as follows below.
MPEP 2106 and the following USPTO website provide further explanation and case law citations: www.uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter? -- MPEP 2106.I and 2106.03
[Step 1: claims 1-17: YES]
Step 2A, 1st prong: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea? -- abstract idea -- MPEP 2106.I and 2106.04
Preliminarily, in a 1st prong of Step 2A, elements of independent claim 1 are interpreted as directed to the abstract idea of analyzing genomics data including the JE elements of "computing...," each of which, including all recitation within each listed element, in at least some embodiments within a BRI, involves only manipulation of data. While manipulation of data is not per se directed to an abstract idea, in this instance the above-identified elements are directed to the abstract ideas identified below.
BRIs of the claims also are analogous to an abstract idea in the form of a mathematical concept, including mathematical relationships and calculations, as found in the following case law, as cited and discussed above: collecting information, analyzing it, and displaying certain results of the collection and analysis (Electric Power Group) and/or obtaining and comparing intangible data (e.g. Cybersource, Ambry and Myriad CAFC) and/or execution of an algorithm to implement mathematical relationships and/or formulas, including image processing (e.g. TLI, Digitech, Benson, Flook, Diehr, FuzzySharp, In re Grams and In re Abele all as cited in MPEP 2106).
Instant examples of math concepts include correcting for covariates (e.g. claim 8), association calculation (e.g. claim 8), P-value correction (e.g. claim 8), W and H matrices and lambda term computations (e.g claim 10), the same or similar computations inherent to computational genomics analysis (claims 1, 11 and 17), etc.
The preceding case law examples are cited for the basic form of their identified abstract ideas, and analogy to these example abstract ideas need not be within the same technology field, 101 analysis generally being assumed to be neutral with respect to technology field.
Regarding inherency of abstract ideas, MPEP 2106.04.II.A.1 includes: "the claims in Alice Corp. v. CLS Bank, 'described' the concept of intermediated settlement without ever explicitly using the words 'intermediated' or 'settlement'" (emphasis added, p. 1). Similarly, inherency can effectively be recitation, as in, for example, "By claiming simply 'crystalline paroxetine hydrochloride hemihydrate' with no reference to how it was produced, SKB effectively claimed 'crystalline paroxetine hydrochloride hemihydrate whether non-naturally occurring or arising through natural conversion.' Claim 1, as issued, therefore combines patentable and unpatentable subject matter, and is invalid under Section 101." (capitalization added, SmithKline Beecham Corp. v. Apotex Corp., 365 F.3d 1306, 1321-33, Fed. Cir. 2004).
In the instant type of data processing claims, the specification is not merely adding background explanation as to how a claimed process works, e.g. a physical process based on, involving or further explained by abstract ideas and natural laws. Rather, the specification is detailing the only disclosed way that a programmer may proceed from the recited inputs to the recited outputs, e.g. through actual performance of the disclosed judicial exceptions (JEs).
Regarding the "Meaning of 'Recites,'" MPEP 2106.04.II.A.1 states:
In Prong One examiners evaluate whether the claim recites a judicial exception, i.e. whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim. While the terms "set forth" and "described" are thus both equated with "recite", their different language is intended to indicate that there are two ways in which an exception can be recited in a claim. For instance, the claims in Diehr, 450 U.S. at 178 n. 2, 179 n.5, 191-92, 209 USPQ at 4-5 (1981), clearly stated a mathematical equation in the repetitively calculating step, and the claims in Mayo, 566 U.S. 66, 75-77, 101 USPQ2d 1961, 1967-68 (2012), clearly stated laws of nature in the wherein clause, such that the claims "set forth" an identifiable judicial exception. Alternatively, the claims in Alice Corp., 573 U.S. at 218, 110 USPQ2d at 1982, described the concept of intermediated settlement without ever explicitly using the words "intermediated" or "settlement."
While the "set forth" language approximates explicit recitation, it also is fundamental that all recitation must be interpreted and that to be patent eligible a claim must satisfy 101 according to its properly interpreted scope, e.g. for all embodiments on which the claim reads, e.g. according to any inherency pertinent to a given claim and disclosure accompanying that claim, i.e. consistent with the "described" meaning of "recites" as in the MPEP. Thus, within a BRI, the identified abstract idea elements read on one or more embodiments which only involve manipulation of data. It is not clear than any improvement argument clearly on the record causes a claim not to be directed to a JE for all embodiments within the scope of the claim.
As in Alice (at 306, as cited in the MPEP above) and Bilski (as cited in Alice, id), an abstract idea may comprise multiple abstract elements or steps (i.e. from Alice: "a series of steps" at 306) and need not be a single equation, relationship or principle.
It is not clear that the identified elements must represent other than an abstract idea according to any relevant analysis or case law.
[Step 2A, 1st prong, abstract idea: claims 1-17: YES]
Step 2A, 2nd prong: If the claims recite a judicial exception under the 1st prong, then is the judicial exception integrated into a practical application? -- MPEP 2106.I and 2106.04(d)
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
In Step 2A, 1st prong above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In Step 2B below, any remaining steps and/or elements are therefore in addition to the identified JE(s). Any such additional steps and additional elements are further discussed in Step 2B.
Here in Step 2A, 2nd prong, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
At this point in examination it is not yet the case that any of the Step 2A, 2nd prong considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of 1. an improvement, 2. treatment, 3. a particular machine or 4. a transformation is clear in the record.
For example, regarding the first consideration at MPEP 2106.04(d)(1), the record, including for example the specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field. The claims do not yet clearly result in such an improvement (e.g. specification: p. 8, last para.; p. 10, 1st and last paras.).
[Step 2A, 2nd prong: claims 1-17: NO]
Step 2B: Do the claims recite a non-conventional arrangement of additional elements in addition to the identified JEs? -- MPEP 2106.I and 2106.05
Addressing the second Mayo/Alice question, all elements of claims 1-17 are part of one or more identified JEs (as described above), except for elements identified here as conventional elements in addition to the above judicial exceptions:
Addressing claim 1, the recited "receiving...," "storing...," "passing..." and "outputting..." are conventional elements of a laboratory and/or computing environment and/or conventional data gathering/input/output elements, as exemplified in MPEP 2106.05(d).II and 2106.05(f-g). Data gathering does not impose any meaningful limitation on the judicial exceptions or on how the judicial exceptions are performed. Data gathering is insufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)). For example, a "wireless communication link..." is a conventional element of a laboratory and/or computing environment, as exemplified at MPEP 2106.05(f), (1), iii and 2106.05(h), 4th para.
Additionally, the above additional elements are interpreted as conventional as evidenced by the art cited in the above art rejections.
Claims 2-17 are analyzed similarly.
It is emphasized that, outside of an improvement argument, analysis of what is conventional generally pertains to the above-identified additional elements and not to elements identified as part of a JE.
[Step 2B: claims 1-17: NO]
Summary and conclusion regarding claims 1-17
Summing up the above analysis of claims 1-17, each viewed as a whole and considering all elements individually and in combination, no claim recites limitations that transform the claim, finally interpreted as directed to the identified JE(s), into patent eligible subject matter, and it is not clear that any claim is sufficiently analogous to controlling case law identifying an example of an eligible claim.
Citations to art
In the above citations to documents in the art, rejections refer to the portions of each document cited as example portions as well as to the entirety of each document, unless otherwise noted in the situation of lengthy, multi-subject documents. Other passages not specifically cited within a document may apply as well.
Conclusion
No claim is allowed.
A shortened statutory period for reply is set to expire THREE MONTHS from the mailing date of this communication.
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The examiner for this Office action, G. Steven Vanni, may be contacted at:
(571) 272-3855 Tu-F 8-7 (ET).
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D. Riggs, II, may be reached at (571) 270-3062.
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686