DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Status of claims
Canceled:
none
Pending:
1-22
Withdrawn:
none
Examined:
1-22
Independent:
1 and 10
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
x
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
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
x
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed on the 12/6/2021 filing receipt, this application claims priority to no earlier than 2/6/2014. 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. 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 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 1-22 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
1, 10
allocating memory for a bit array
Since there is a later-instantiated "a set of secondary bit arrays" (claim 3), then this first bit array should recite "a first bit array" or "a primary bit array" or some equivalent.
The same issue occurs in claim 10 regarding "initializing a bit array."
1
for a set...
into a bit array
The relationship is unclear between this instantiation of "a bit array" and the preceding instantiation in the "allocating" step.
Similarly, claims 2 are rejected for again instantiating "a bit array."
1
a set of hash operators
The relationship is unclear between the two instantiations in the "applying" steps after both "for a set of key-value mappings..." and "extracting a k-mer..."
1
bitwise...
the set of binary mask
It appears that "mask" should be plural after "set."
1
retrieving a set of binary masks
The relationship is unclear between this instantiation of "a set of binary masks" vs. the preceding "a binary bit mask."
2
an key-value mapping
First, the article "a" rather than "an" should precede "key."
Second, the relationship is unclear between this instantiation and the preceding "for a set of key-value mappings..."
2-9
the first bit array
The relationship is unclear between this instance in claim 2 and preceding instances of "bit array."
Claims 3 are rejected similarly regarding its recitation of "the bit array," and this issue should be reviewed throughout claims 2-9.
It should also be verified that all instances of "the bit array" have clear and singular antecedent.
4
the secondary bit array mode
Requires but lacks antecedent, noting the preceding instantiation was "a secondary array mode"
4
a second set of indexes
The relationship is unclear between this instantiation the preceding instantiation in claim 1.
4
the secondary bit array
Requires but lacks antecedent
4
the bit array in memory
Antecedent is unclear, there being multiple preceding instantiations.
5
a set of indexes
Antecedent is unclear
5
a first subset of hash operators
The relationships are unclear versus the claim 1 "a set of hash operators" and versus the two instances of this same recitation in claim 5.
5
a second subset of hash operators
The relationships are unclear versus the claim 1 "a set of hash operators" and versus the two instances of this same recitation in claim 5.
5
wherein obtaining a set of indexes when inserting
The "wherein" clause requires antecedent, but the antecedent unclear.
5
wherein obtaining the set of query indexes during lookup
The "wherein" clause requires antecedent, but the antecedent unclear.
5
the set of query indexes
Requires but lacks clear antecedent
5
the biological sequence query key
Requires but lacks clear antecedent
5
the second set of query indexes
Requires but lacks clear antecedent
10
a reference key-value element maps a key to a value
The relationship is unclear to the preceding "a set of..." This instance may be revised to "[[a]]each reference..."
11
a key-value element
The relationship is unclear between this instantiation and the instantiation in claim 1.
10
applying... the key
It appears that multiple keys have been instantiated such that it is unclear which is antecedent to this singular instance.
10
executing... the value
It appears that multiple values have been instantiated such that it is unclear which is antecedent to this singular instance.
10
applying... to obtain a set of indexes
Since there is a later-instantiated "a second set of indexes," then this first set should recite "a first set of indexes."
10
applying... a second set of query indexes
There does not appear to be a first set.
11
a key-value element
The relationship is unclear between this instantiation and that in claim 10.
11
in response to detecting an indeterminate error scenario
The relationship is unclear between this instantiation and that earlier in claim 11.
12
a set of secondary bit arrays
The relationship is unclear between this instantiation and the already instantiated "a second bit array" (claim 11).
13, 17-21
the bit array
In claim 13, the relationship is unclear between this instance of bit array versus the previously recited "a bit array" (claim 1) and "a secondary bit array" (claim 11).
Claims 17-21 are rejected similarly.
15
the set of key-value elements
Requires but lacks clear antecedent
18
setting bit mask weight
A grammatical article is needed before "bit."
22
a reference key-value element
The relationship is unclear between this instantiation and those preceding.
Each issue above causes the scope of the claim to be indefinite because it is unclear how the claim elements relate to each other and to the claim as a whole.
Claim rejections - 112/a
The following is a quotation of 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.
Written description
Claims 1-22 are rejected under 112/a as failing to comply with the written description requirement. The claims read on subject matter which is not described in the specification in such a way as to reasonably convey to PHOSITA that the inventors, at the time the application was filed, had possession of the claimed invention. Claims depending from rejected claims are rejected similarly, unless otherwise noted. With regard to any suggested amendment(s) below to overcome a rejection, equivalent amendments also would be acceptable.
Claim 1 recites "a bit array," "a set of key-value mappings between a biological sequence k-mer and a characterization value" and "encoding the characterization value to a binary bit mask of fixed-weight," in which "biological characterizations can be based on nucleotides or protein sequence data" (specification: [32]) and "The system and method for characterizing biological sequence data through a probabilistic data structure of an embodiment functions to employ a probabilistic data structure." It is not clear, however, that there is written description support for any embodiment of the recited methods other than either "nucleotides or protein sequence data" and using "a probabilistic data structure." Independent claims 1 and 10, however, are not so limited such that the claims read on embodiments not clearly supported.
Claims 2-22 are rejected similarly.
As appropriate, these rejections may be overcome, for example, (i) by narrowing to supported embodiments and/or (ii) by clarifying on the record where support can be found and how that support relates to the broader scope of the recitations.
Claims 7-8 address the nucleotide or protein limitations but do not address the probabilistic data structure limitation. Both aspects appear necessary to satisfy 112/a.
MPEP 2163 pertains.
Claim interpretations
The following claim interpretations apply:
Claim
Recitation
Comment
14
a second secondary
bit array
While the recitation is potentially confusing, it is supported at [99].
Subject matter clear of the prior art
Claims 1-22 are clear of the prior art, for example the art cited on the 12/3/2021 IDS and as found in the attached search histories. The recited structure and methods most closely relate, in mathematical form, to prior art teaching "mathematical and performance properties [of] the well-known probabilistic data structure the Bloom filters" (specification of provisional application 61/936,521 at p. 1). However, "In contrast to Bloom filters, which only support set membership queries, B-fields support associating a set of x, y key-value pairs ... " (id.), which property enables the novel storage and look-up functions of the instant claims. Additionally, the instantly recited methods are comparable to techniques using a "Hash table," an "Array of tuple" and a "Binary tree," as shown in the table at p. 22 of Applicant's 1 May 2017 remarks in parent application 14/615,672, now patent 9,892,237. However, no prior art was found teaching the recited data structures, in particular not with the recited bit-level logical operations, with their inherent computational efficiency (61/936,521 at p. 1).
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 1-22 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 1-22: 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 resolving queries of a biological sequence data source including the JE elements of "allocating...," "initializing...," "...inserting..., by: ...," "selecting..." and "extracting..., by: ...," 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.
Claim 10 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.
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 applying hash operators, encoding, ORing, etc., as well as relationships inherent in recitations as the only supported embodiments.
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 and 10: 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: [43]).
[Step 2A, 2nd prong: claims 1 and 10: 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 10 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 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)).
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 10: NO]
Summary and conclusion regarding claims 1 and 10
Summing up the above analysis of claims 1 and 10, 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 2-9 and 11-22 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.
Nonstatutory double patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine to prevent the improper timewise extension of the "right to exclude" granted by a patent and to prevent multiple suits against an accused infringer by different assignees of the same invention (MPEP 804.II.B, 1st para.). A nonstatutory double patenting rejection is appropriate where the conflicting claims (instant v. reference) are not identical, but an examined-application claim (instant claim) is not patentably distinct from a reference claim because the instant claim is either anticipated by, or would have been obvious over, the reference claim (MPEP 804.II.B, 2nd para.).
In cases of double patenting rejections versus reference claims of pending applications, as opposed to claims of an issued patent, the rejections are provisional because the reference claims have not been patented. Presently, no rejections are provisional.
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the application or patent of the reference claim either is shown to be commonly owned with the instant application or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. A registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must comply fully with 37 CFR 3.73(b).
Applicant may wish to consider electronically filing a terminal disclaimer (MPEP 1490.V pertains, along with https://www.uspto.gov/patents-application-process/applying-online/eterminal-disclaimer). Electronic filing may lead to faster approval of the disclaimer. Also, if filing electronically, Applicant is encouraged to notify the examiner by telephone so that examination may resume more quickly.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used.
A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Double patenting rejections of instant claims 1-22
Instant claims 1-22 are rejected on the grounds of nonstatutory double patenting as unpatentable over one or more claims in reference patent 9,892,237 (from application 14/615,672) in view of Brudno, Pieterse and Lin (each as cited on the 12/3/2021 IDS).
The reference patent as well as the instant application recite claims which involve initializing a bit array with key-value mappings, applying hash operators and encoding, processing a query and calculating a k-mer characterization.
Although the reference claims are not identical to the instant claims, in a BRI they also are not patentably distinct from the instant claims: either (i) because the instant claims recite obviously equivalent or broader limitations in comparison to the reference claims or (ii) because the instant claims recite limitations which are obvious over the cited art. It is not clear that the instant claims recite limitations which are narrower than limitations in the reference claims.
It would have been obvious in view of the cited art to modify reference claims to arrive at the rejected instant claims. Either the instant limitations are interpreted as reading on a reference limitation, or the instant limitations would have been obvious in view of the cited art. That is, to the extent that any instant claims are narrower than reference claims, then any such narrowing would have been obvious over the cited art.
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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