DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Status of claims
Canceled:
none
Pending:
1-21
Withdrawn:
none
Examined:
1-21
Independent:
1, 11 and 21
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 or column:line
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed on the 8/20/2024 filing receipt, this application claims priority to no earlier than 6/25/2021. All claims have been interpreted as being accorded this priority date.
Objection to the specification: title
The title should be amended to more specifically reflect the claims, particularly the independent claims and referencing steps/elements: setting the context of the invention, particular to all claims, and distinguishing the instant application from any related applications, for example a title including terms such as: genetic, sequence, filtering, identifying matches, etc. The title should be "descriptive" and "as... specific as possible" (MPEP 606, 1st para. and 37 CFR 1.72; also MPEP 606.01 pertains).
Claim objections
Claim 2 is 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
2
and-wherein
Probably "and[[-]]_wherein"
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 1-21 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, 11, 21
filtering...
exclude known sequences not to be of interest
Not interpretable; possible "...known not to be of interest
1, 11, 21
filtering...
exclude at least
one sequence portion...
results in a filtered sequence subset that contains sequences
The recited "at least one" appears not to correspond to the later recited "contains sequences" plural. Possibly "at least one" should read "two or more."
1, 11, 21
filtering...
identity to the known sequences not to be of interest;
Not interpretable; possible "...known not to be of interest;"
6
further comprising retrieving the stored data includes verifying...
Not interpretable at least for lack of antecedent as to the recited "retrieving the stored data includes..."
8, 18
the known pathogen
In claim 8, the recitation requires but lacks clear antecedent. Possibly claim 8 should depend from claim 7.
Claim 18 is rejected similarly.
9, 19
the known pathogen that correspond to the matches
In claim 9, the recitation requires but lacks clear antecedent. Possibly claim 9 should depend from claim 7.
Claim 18 is rejected similarly.
10, 20
the known pathogen
In claim 9, the recitation requires but lacks clear antecedent. Possibly claim 10 should depend from claim 7.
Claim 18 is rejected similarly.
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 1-21
Claims 1-21 are rejected under 35 USC 103 as unpatentable over Rolfe (WO 2013-173795 as cited on the 8/7/2024).
Regarding claims 1-4, 7-14 and 17-21, Rolfe anticipates each element and step of each claim by teaching a method of updating in real time a database of pathogenic microorganisms to create a bio-surveillance system. The method involves identifying a match between a sequence identified in the sample and a database comprising stored sequences of known pathogenic organisms, wherein the system communicates a match through a network and stores any unmatched sequence lo the database in real like. The database may be a centralized database located remotely from where the sample is obtained (Rolfe: [21-22]).
Rolfe further discloses that the sequences identified do not belong to an exclusion set. The exclusion set may be the human genome, genomes of common human microflora or commensal organisms and from sequenced genomes from commensal, non-virulent, or non-pathogenic viral, eukaryotic, prokaryotic, and archaeal organisms. The sequences obtained may comprise barcodes which allow identification of the sequences in the database (Rolfe: [51]).
Rolfe further discloses that the sequences are filtered to eliminate those that specifically hybridize to a sequence in a genome in the exclusion set of genomes, e.g., comprising the genome of the subject (in the case of a biological sample) and sequenced genomes of organisms other than the organism of interest, including viruses, bacteria, archaea, fungi, and other eukaryotes (Rolfe: [101]).
Rolfe teaches that the output from the database may be an encrypted file (Rolfe: [171]).
To the extent that the limitations within claims 1, 11 and 21 are taught individually but are not explicitly taught with the recited relationships and sequencing among limitations, then in the absence of a secondary consideration to the contrary, it would have been prima facie obvious to PHOSITA to try the recited combination of limitations as those limitations are taught individually as described above. Trying the recited combinations would have been examples of combining prior art elements, elements taught within the same reference, according to known methods to yield predictable results and choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success (MPEP 2143.I pertains).
Regarding claims 5-6 and 15-16, Rolfe teaches query sequences (Rolfe: [6]) and encryption (Rolfe: [171]).
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 1-21 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 1-21: 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 data to identify a pathogenic sequence including the JE elements of "filtering...," "identifying..." and "storing...," 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.
Claims 11 and 21 are 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, 11 and 21: 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: [2, 49]).
[Step 2A, 2nd prong: claims 1, 11 and 21: 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, 11 and 21 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 "receiving" is a conventional element 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 significant 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)).
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, 11 and 21: NO]
Summary and conclusion regarding claims 1, 11 and 21
Summing up the above analysis of claims 1, 11 and 21, 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 2-10 and 12-20 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.
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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
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