DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Status of claims
Canceled:
none
Pending:
1-34
Withdrawn:
4-5, 8, 10-31 and 34
Examined:
1-3, 6-7, 9 and 32-33
Independent:
1 (withdrawn 18)
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.
x
101 Other
N:N
page:line or column:line
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed on the 1/31/2023 filing receipt, this application claims priority to no earlier than 3/12/2020. All claims have been interpreted as being accorded this priority date.
Restriction/election
Applicant’s election with traverse in the 4/15/2026 reply is acknowledged.
Applicant timely traversed the restriction requirement. The traversal is on the ground(s) that "...the search and examination of the entire application could be made without serious burden" (applicant 4/15/2026 remarks). This assertion is not found persuasive because there appears to be extensive art in the relevant fields of genetics and sequence analytics and associated analytical and statistical methods, and the various claim limitations are taught in various and disparate portions of that art and/or would not clearly be expected to be found within the same or closely related references retrievable with the same or similar search parameters. This same reasoning applies to the group and species restriction requirements. The requirements are deemed proper for the above reasons and as described in the 2/17/2026 restriction requirement, and the requirements are made final.
Applicant may request an interview if it becomes clear during examination that examination would be advanced by relaxing the restriction requirement to re-join withdrawn subject matter, particularly with regard to a species election.
As listed above, claims are withdrawn as drawn to nonelected inventions pursuant to 37 CFR 1.142(b), and the remaining claims have been examined as listed above.
Objections to the drawings
The 9/12/2022 supplemental drawings are objected to because they contain sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application does not comply with the requirements of 37 CFR §§ 1.821-1.825 for the following reasons:
Nucleotide sequences appear in FIG. 17 without the sequences being labeled by particular "SEQID" numbers as set forth in 37 CFR § 1.821 (see MPEP § 2422).
Sequences of 10 or more nucleotides must be identified by sequence identification number, and a listing including the sequences must be supplied. It is often convenient to identify sequences in figures by amending the Brief Description of the Drawings section (see MPEP 2422.02).
Applicants are required to comply with all the requirements of 37 CFR 1.821-1.825. Any response to this action which fails to meet these requirements will be non-responsive. The nature of the sequences disclosed in the instant application has allowed an examination on the merits, as follows.
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 1-3, 6-7, 9 and 32-33 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
involving
The recited "involving" is a term of relative or vague degree or form of association, neither defined in the specification nor having a well-known and sufficiently particular definition in the art and in the instant context. (MPEP 2173.05(b) pertains.)
1
the genome
Requires but lacks antecedent; possibly "a genome"
1, 7, 33
...involving:
partial... sequencing... strain;
applying...bacterial species.
The relationship between the two list elements is unclear for lack of a grammatical article specifying the relationship, e.g. as to "and" vs. "or." A two-element list of two steps "...sequencing..." or "...applying..." is recited after "involving:...," and a grammatical conjunction should appear between the two steps.
Similar issues occur in claims 7 and 33, also rendering those claims indefinite.
1
the constituent genome sequences
The recitation requires but lacks antecedent at least because the preceding instance of "genome sequences" did not recite "constituent." Also, the interpretation of "constituent" in the recited context is unclear, e.g. as to "constituent" with respect to what other element.
1, 3, 9
their co-occurrence rates in the genome of the bacterial species
In claim 1, the relationship is unclear between this instance of "co-occurrence rates" plural and the previously instantiated "co-occurrence rate" singular. Claims 3 and 9 are similarly indefinite. The relationships may be clarified among all instances of "co-occurrence rate" singular and plural.
1
...a bacterial strain...
the bacterial species...
The relationship is unclear between instances of "strain" vs. "species," including all singular and all plural instances.
2
a first subset of the genome sequences is a set of unclustered variables
The relationship is unclear between "genome sequences" and "set of unclustered variables" at least because it is unclear how "sequences" relate to "variables."
2
a first phenotypic trait prediction model
The relationship is unclear between the claim-1-recited "predetermined model" and this "model" of claim 2.
3
a co-occurrence rate
The relationship is unclear between this instance and that of claim 1. Possibly "first" and "second" should be recited.
3
a predetermined threshold
The relationship is unclear between this instance and that of claim 1. Possibly "first" and "second" should be recited.
32
A computer program product storing computer-executable instructions for the application of a model for predicting a phenotypic trait of the a bacterial strain, the application being as
claimed in claim l.
Each of the following issues individually renders the indefinite:
(i) There is a grammatical error at "...the a..."
(ii) The relationship is unclear between the recited "product" and the recited "...for the application of..." at least because the latter is interpreted as intended use not clearly limiting the "product" or the claim overall.
(iii) The relationship is unclear between claims 32 and 1 at least because interpretation of the claim-32-recited "...the application being as claimed in claim l" is unclear. For example, the first instance of "application" is interpreted as intended use, so that it is unclear what requirement if any is created by the reference to claim 1. Also, claim 1 is directed to a "process" while "application" in claim 32 appears to be an intended use software element. Claim 1 does not recite an "application." Also, regarding any future amendment, it is noted that a claim to a 101 machine or manufacture, in claim 32 a "product," cannot directly recite a process step.
(iv) In claim 32, the recited "the application of a model..." requires but lacks clear antecedent basis.
32-33
a model for predicting a phenotypic trait
In claim 1, the relationship is unclear vs. the same element in claim 1.
The same issue occurs in claim 33 with "a phenotypic trait," "a bacterial strain" and "a predetermined model."
33
a computer unit configured to apply
Claim 33 is to a 101 machine or manufacture, i.e. a "system" in this instance, interpreted by statute according to its claimed physical structure, but it is not clear what is the structure associated with the recited "a computer unit configured to apply..." and similar steps. Therefore, it is not clear whether the claim is limited according to these steps. MPEP 2106.03, 5th-6th paras. pertain. The recited "system" is interpreted as not clearly requiring structure linking the "system" to the recited steps in a structural sense appropriate to a claim to a machine or manufacture. While the recited elements, the "computer unit" may comprise unrecited software storage in some embodiments, it is not clear that all embodiments of these elements must comprise software storage corresponding to the recited process steps. Structure should be recited specifically corresponding to stored software. The recited process steps are not properly claimed without corresponding structure. This rejection might be overcome by, for example, reciting a data storage device, comprised by the "system," and instructions stored therein and configured according to the recited elements and steps. Support should be identified for any such amendment. MPEP 2173.05(p).II pertains regarding a claim directed to both product and process.
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.
Claims 1-3, 9 and 32-33
Claims 1-3, 9 and 32-33 are rejected under 35 USC 103 as unpatentable over Goodrich (as cited on the attached "Notice of References Cited" form 892).
Regarding claims 1-3 and 32-33, Goodrich teaches sequencing as "quality-filtered sequences" (p. 790, §"Twin Data Set").
Goodrich teaches model application as "twin-based ACE model" and "ICC" (p. 791, §"Heritability Estimates for OTUs and Predicted Functions"; also Fig. 2 caption and §"Broad Diversity Comparisons between MZ and DZ Twin Pairs") and sequence groups as "Clusters of Orthologous Groups" (p. S4, §"PICRUSt") and "operational taxonomic units (OTUs...)" (p. 790, §"Microbiome Composition and Richness").
Goodrich teaches thresholding of co-occurrence as "threshold" (p. S3, §"Co-occurrence Network").
Goodrich teaches each of the limitations as described above, however Goodrich does not teach the limitations in a single embodiment in the same, consecutive sequence as recited. It would have been prima facie obvious to try the recited sequence as an example of combining prior art elements taught within the same reference according to known methods to yield predictable results.
Regarding claim 9, Goodrich teaches dendrogram analysis as phylogenetic trees (p. 791, §"Broad Diversity Comparisons between MZ and DZ Twin Pairs" and p. S2, §"Use of the Microbial Phylogeny in Heritability Calculations" and §"Heritability Calculations").
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.
Matter belonging to no statutory category -- claim 32
Claim 32 is rejected under 35 USC 101 because the claimed invention is directed to non-statutory subject matter.
Claim 32 is to a "computer program product," which, without reciting "non-transitory," is not, in all embodiments within a BRI, interpreted as belonging to any category listed in 101. In a BRI, 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 it does not fit within any of the four statutory categories of invention (In re Nuijten, Federal. Circuit, 2006).
As appropriate, this rejection can be overcome by, for example, amending to recite "non-transitory." The claim must comprise at least one clearly physical and non-transitory element. Support should be identified for any such amendment.
Judicial exceptions (JE) to 101 patentability
Claims 1-3, 6-7, 9 and 32-33 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 1-3, 6-7, 9 and 33: YES; claim 32: NO as rejected above]
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 determining a phenotype including the JE element of "applying...," 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.
Claim 33 is analyzed similarly.
BRIs of the claims are analogous to an abstract idea in the form of at least a mental process, at least equivalent to a computer-implemented process, including obtaining and comparing intangible data (e.g. Cybersource, Synopsys and Electric Power Group). In a BRI, it is not clear that the claim embodiments are limited so as to require complexity precluding analogy to a mental process.
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 and 33: 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? -- law of nature -- MPEP 2106.I and 2106.04
Preliminarily, at this 1st step of the analysis, elements of independent claim 1 are directed to a law relating sequence to phenotype, including the JE element of "applying..."
Claim 33 is analyzed similarly.
A BRI of the instant claims is analogous to a law of nature as found, for example, in Mayo (as cited in the MPEP above). 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. It is not clear that the above identified law of nature including the identified elements, taken together and within a BRI, must in all embodiments represent other than a law of nature according to any relevant analysis or case law. Therefore, in answer to the 1st Mayo/Alice question, the above elements are directed to a law of nature.
[Step 2A, 1st prong, natural law: claims 1 and 33: 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: 3:8-12; 7:4-27; 9:1-6).
[Step 2A, 2nd prong: claims 1 and 33: 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 and 33 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:
The recited "sequencing platform" and "computer unit" 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), and as exemplified by Goodrich (as cited on the attached "Notice of References Cited" form 892), and generally it is understood that the examples in the reference are well-known and routine.
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 and 33: NO]
Summary and conclusion regarding claims 1 and 33
Summing up the above analysis of claims 1 and 33, 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.
Remaining claims
Claims 2-3, 6-7 and 9 add elements which also are part of the identified JEs for the same reasons described above regarding the independent claims and therefore do not provide the something significantly more necessary to satisfy 101.
None of the dependent claim elements provides the something significantly more than the identified JE(s) necessary to satisfy 101.
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.
Inquiries
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The Electronic Business Center (EBC) at 866-217-9197 (toll-free) is available for additional questions, and assistance from a Customer Service Representative is available at 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
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
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