DETAILED ACTION
The Applicant’s filing, received 26 May 2022 has been fully considered. The following rejections and/or objections constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 are pending.
Claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 are rejected.
Claims 20, 29, and 36 are objected to.
Priority
This application is a 371 of PCT/IL2019/051300, filed 27 November 2019.
Claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 are given the benefit of priority to PCT/IL2019/051300, filed 27 November 2019.
Therefore, the effective filing date of the claimed invention is 27 November 2019.
Drawings
The drawings received 26 May 2022 are objected to for the following reasons:
the drawings fail to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description:
110.(L-1) in Figures 1A, 2A, 3A, and 3B;
736 (Data-Block Coder) in Figure 6;
738 (Synthesizing Controller) in Figure 6; and
390 (Output the sequence S) in Figure 7D.
Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Information Disclosure Statement
The information disclosure statements (IDS) received 12 July 2022 and 03 June 2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all 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 by the examiner on form PTO-892, they have not been considered.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) are:
“a sequencing control module” in claims 27 and 29;
“a data inference processing module” in claims 27 and 30;
“a container module” in claim 36;
“a harvesting module” in claim 39; and
“a control unit” in claims 36 and 41.
Because these claim limitation(s) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, they are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
The written description discloses a corresponding structure for the non-structural generic placeholder:
“a container module” in claim 36 at page 10, line 3 (i.e., a plurality of containers) and at page 38, lines 22-32 (i.e., building-block containers).
The written description does not disclose a corresponding structure for the non-structural generic placeholder:
“a sequencing control module” in claims 27 and 29;
“a data inference processing module” in claims 27 and 30;
“a harvesting module” in claim 39; and
“a control unit” in claims 36 and 41.
If applicant does not intend to have these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Objections
Claim 20 is objected to because of the following informalities: The backward slash between the word “sequences” and the word “of” in line seven should be deleted.
Claim 29 is objected to because of the following informalities: The word “and” at the end of line eight should be deleted.
Claim 36 is objected to because of the following informalities: The word “synthesize” in line 28 should be deleted and replaced with the word “synthesis.”
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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 of carrying out his invention.
Claims 27, 29, 30, 36, 39, and 41 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 27 and 29 recite the limitation “a sequencing control module” however the disclosure does not clearly link any structure for the “sequencing control module” as required by MPEP 2181. For example, the disclosure describes the function of the “sequencing control module” (e.g., at page 42, lines 20-25) but does not link any structure to the functions.
Claims 29 and 30 are rejected for depending from claim 27 and failing to remedy the failure to comply with the written description requirement.
Claims 27 and 30 recite the limitation “a data inference processing module” however the disclosure does not clearly link any structure for the “data inference processing module” as required by MPEP 2181. For example, the disclosure describes the function of the “data inference processing module” (e.g., at page 8, lines 7-9) but does not link any structure to the functions.
Claim 29 is rejected for depending from claim 27 and failing to remedy the failure to comply with the written description requirement.
Claims 36 and 41 recite the limitation “a control unit” however the disclosure does not clearly link any structure for the “control unit” as required by MPEP 2181. For example, the disclosure describes the function of the “control unit” (e.g., at page 10, lines 10-26) but does not link any structure to the functions.
Claims 39 and 41 are rejected for depending from claim 36 and failing to remedy the failure to comply with the written description requirement.
Claim 39 recites the limitation “a harvesting module” however the disclosure does not clearly link any structure for the “harvesting module” as required by MPEP 2181. For example, the disclosure describes the function of the “harvesting module” (e.g., at page 41, lines 1-9) but does not link any structure to the functions.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites the limitation "the Z types" in line thirteen. There is insufficient antecedent basis for this limitation in the claim.
Claims 2, 3, 5, 7, 8, 13, 14, and 17 are indefinite for depending from claim 1 and for failing to remedy the indefiniteness of claim 1.
Claim 45 is indefinite for reciting the system according to claim 1, i.e., the limitation "the Z types" because there is insufficient antecedent basis for this limitation in the claim.
Claim 2 is indefinite for reciting “enabling robust and efficient sequencing protocol” because it is unclear as to what the metes and bounds are with regard to the terms “robust” and “efficient.”
Claim 5 recites the limitation "the Z different types" in line two. There is insufficient antecedent basis for this limitation in the claim.
Claims 5 and 21 are indefinite for reciting “H1”. Acronyms and/or abbreviations should be fully defined and recited at least one time in a given set of claims.
Claim 5 is indefinite for reciting “robust reading” because it is unclear as to what the metes and bounds are with regard to the term “robust.”
Claim 7 is indefinite for reciting “πn” in the limitation “each valid encoded alphabet letter πn of the sequence S = (π1, π2, …, πn…, πN-1, πN),” because it is not clear as to whether “πn” has the same meaning as “πn”.
Claim 8 is indefinite for depending from claim 7 and for failing to remedy the indefiniteness of claim 7.
Claim 7 recites the limitation "the space spanned by…" in line four. There is insufficient antecedent basis for this limitation in the claim, and it is further not clear what the term “space” means (e.g., distance and/or area and/or volume).
Claim 8 is indefinite for depending from claim 7 and for failing to remedy the indefiniteness of claim 7.
Claims 8 and 22 are indefinite for reciting “H2”. Acronyms and/or abbreviations should be fully defined and recited at least one time in a given set of claims.
Claim 20 recites the limitation "the data encoding sections" in line six. There is insufficient antecedent basis for this limitation in the claim.
Claims 21, 22, 24, 26, 27, 29, and 30 are indefinite for depending from claim 20 and for failing to remedy the indefiniteness of claim 20.
Claim 20 recites the limitation "the Z types" in line nineteen. There is insufficient antecedent basis for this limitation in the claim.
Claims 21, 22, 24, 26, 27, 29, and 30 are indefinite for depending from claim 20 and for failing to remedy the indefiniteness of claim 20.
Claims 24 and 26 are indefinite for reciting “πn” in the limitation “the encoded alphabet letters πn” (in line five of claim 24, and in line eleven of claim 26), because it is not clear as to whether “πn” has the same meaning as “πn” since claim 20 at step (iii) recites the limitation “determining encoded alphabet letters πn of a sequence S = (π1, π2, …, πn…, πN-1, πN) encoded by….”
Claim 26 is indefinite for reciting “ST”. Acronyms and/or abbreviations should be fully defined and recited at least one time in a given set of claims.
Claim 33 recites the limitation "the basic molecular building-blocks" in lines three and four. There is insufficient antecedent basis for this limitation in the claim.
Claim 36 is indefinite for reciting “πn” in the limitation “each letter πn of the sequence S” in line 27, because it is not clear as to whether “πn” has the same meaning as “πn” since the claim recites “a sequence of letters S= {πn} | n=1 to N” at lines 20-21.
Claims 39 and 41 are indefinite for depending from claim 36 and for failing to remedy the indefiniteness of claim 36.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter?
Claims 1-3, 5, 7, 8, 13, 14, and 17 recite a molecular data storage system (i.e., a machine or manufacture) for encoding one or more data-blocks; claims 20-22, 24, and 26 recite a method (i.e., a process) for reading data stored in a molecular data storage system; claims 27, 29, and 30 recite a data reader system (i.e., a machine or manufacture) adapted to implement the method according to claim 20; claims 31-33 and 35 recite a method (i.e., a process) for fabricating a molecular data storage system; claims 36, 39, and 41 recite a molecular data storage fabrication system (i.e., a machine or manufacture) adapted to implement the method according to claim 31; and claim 45 recites a molecular label (i.e., a machine or manufacture) comprising the data storage system according to claim 1.
Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes 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.
Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
encoding a respective data-block of the one or more data-blocks (i.e., mental processes and mathematical concepts);
the data encoding sections of the molecular sequences of the population collectively encode a sequence of encoded alphabet letters S = (π1, π2, …, πn…, πN-1, πN) (i.e., mental processes and mathematical concepts); and
each valid encoded alphabet letter πn at location n of the sequence S of alphabet letters is characterized by occurrence of a predetermined plurality of different types of short k-mers of the building-block-set in a corresponding location n along the data encoding sections of the plurality of molecular sequences of said population (i.e., mental processes).
Independent claim 20 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
defining a data-block (i.e., mental processes);
determining, per each location n of 1 to N locations in the data encoding sections of sequenced molecular sequences/ of said population, an observed binary vector Xn of dimension Z, whereby each binary component indexed z of 1 to Z binary components of the observed binary vector Xn is indicative of whether a corresponding building block Ez of a building-block-set {Ez}|z=1 to z was sequenced at the location n corresponding to the index of said binary vector Xn along any of the sequenced molecular sequences of said population (i.e., mental processes and mathematical concepts);
respective data encoding sections of similar predetermined length N of short k-mers serving as data encoding building blocks and forming a building-block-set {Ez}|z=1 to z consisting of a number Z of different preselected short k-mers by which data of the data-block is encoded, wherein all the Z types of short k-mers in said building-block-set have a similar predetermined size k≥2 of bases (i.e., mental processes and mathematical concepts); and
determining encoded alphabet letters πn of a sequence S = (π1, π2, …, πn…, πN-1, πN) encoded by said n = 1 to N locations by associating each observed binary vector Xn of each of said n = 1 to N locations, to one of alphabet letters {σm} of a predetermined alphabet ∑ ≡ {σm}|m=1 to M; whereby each letter σm of the alphabet ∑ is defined by a binary occurrence vector of size Z indicative of an occurrence of building blocks of said building-block-set {Ez} in the letter; said associating comprises mapping the observed binary vector Xn at each location n to one of the letters {σm}|m=1 to M of the alphabet ∑ by determining a match between the observed binary vector Xn and the binary vector definition of the letters (i.e., mental processes and mathematical concepts).
Independent claim 27 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the abstract ideas recited by independent claim 20 as noted above (i.e., mental processes and mathematical concepts) and in particular:
step (i) defining a data-block (i.e., mental processes);
step (ii) determining, per each location n of 1 to N locations in the data encoding sections of sequenced molecular sequences/ of said population, an observed binary vector Xn of dimension Z, whereby each binary component indexed z of 1 to Z binary components of the observed binary vector Xn is indicative of whether a corresponding building block Ez of a building-block-set {Ez}|z=1 to z was sequenced at the location n corresponding to the index of said binary vector Xn along any of the sequenced molecular sequences of said population (i.e., mental processes and mathematical concepts);
respective data encoding sections of similar predetermined length N of short k-mers serving as data encoding building blocks and forming a building-block-set {Ez}|z=1 to z consisting of a number Z of different preselected short k-mers by which data of the data-block is encoded, wherein all the Z types of short k-mers in said building-block-set have a similar predetermined size k≥2 of bases (i.e., mental processes and mathematical concepts); and
step (iii) determining encoded alphabet letters πn of a sequence S = (π1, π2, …, πn…, πN-1, πN) encoded by said n = 1 to N locations by associating each observed binary vector Xn of each of said n = 1 to N locations, to one of alphabet letters {σm} of a predetermined alphabet ∑ ≡ {σm}|m=1 to M; whereby each letter σm of the alphabet ∑ is defined by a binary occurrence vector of size Z indicative of an occurrence of building blocks of said building-block-set {Ez} in the letter; said associating comprises mapping the observed binary vector Xn at each location n to one of the letters {σm}|m=1 to M of the alphabet ∑ by determining a match between the observed binary vector Xn and the binary vector definition of the letters (i.e., mental processes and mathematical concepts).
Independent claim 31 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
one or more blocks of data are coded by a sequence of letters S = {πn}|n=1 to N of an alphabet ∑ ≡ {σm}|m=1 to M (i.e., mental processes);
the letters {σm}|m=1 to M of the alphabet ∑ are represented as binary occurrence vectors defined over a space spanned by Z different types of short k-mers of length k>1, which serve as data encoding molecular building blocks {En}|n=1 to Z (i.e., mental processes and mathematical concepts);
sequences of letters S = {πn}|n=1 to N of said block of data (i.e., mental processes); and
binary vector representing the letter πn (i.e., mental processes and mathematical concepts).
Independent claim 36 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the abstract ideas recited by independent claim 31 as noted above (i.e., mental processes and mathematical concepts) and in particular:
at step (b) one or more blocks of data are coded by a sequence of letters S = {πn}|n=1 to N of an alphabet ∑ ≡ {σm}|m=1 to M (i.e., mental processes and mathematical concepts);
at step (c) the letters {σm}|m=1 to M of the alphabet ∑ are represented as binary occurrence vectors defined over a space spanned by Z different types of short k-mers of length k>1, which serve as data encoding molecular building blocks {En}|n=1 to Z (i.e., mental processes and mathematical concepts); and
indicated to be occurring by the binary vector representing the letter πn (i.e., mental processes and mathematical concepts);
at least one block of data is coded by a sequence of letters S= {πn}|n=1 to N of an alphabet ∑ ≡ {σm}|m=1 to M; and wherein the letters {σm}|m=1 to M of the alphabet ∑ are represented as binary vectors (occurrence vectors) defined over a space spanned by Z different types of said data encoding molecular building blocks {En}|n=1 to Z (i.e., mental processes and mathematical concepts); and
indicated to be occurring by the binary vector representing the letter πn (i.e., mental processes and mathematical concepts)
Independent claim 45 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the abstract ideas recited in claim 1 (i.e., mental processes and mathematical concepts); and
at least one data-block is being respectively encoded (i.e., mental processes and mathematical concepts).
Dependent claims 2, 3, 5, 7, 8, 13, 14, 21, 22, 33, 24, 26, 29, 30, 32, and 41 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 2 further recites:
each valid encoded alphabet letter πn at location n of the sequence S of alphabet letters is further characterized by occurrence of a predetermined exact number Y of the different types of short k-mers of the building-block-set in said corresponding location n in the data encoding sections, said predetermined exact number Y being the same for all the valid encoded alphabet letters (i.e., mental processes); and
enabling robust and efficient sequencing protocol by validating a letter encoded at said location n based on equality between said predetermined exact number Y and an actual number of Y' of different types of short k-mers observed at said corresponding location n of said data encoding sections (i.e., mental processes and mathematical concepts).
Dependent claim 3 further recites:
characterized in that all the different types of preselected short k-mers in said building-block-set have a similar predetermined size k≤20 of bases, thereby facilitating production scale data storage via molecular synthesis and low physical density (i.e., mental processes).
Dependent claim 5 further recites:
the Z different types of short k-mers in said building-block-set are characterized in that a hamming distance between each short k-mer in said building-block-set and any other short k-mer in said building-block-set is greater or equal to a certain first H1 threshold of minimal hamming distance, whereby said first threshold satisfies H1≥2, thereby enabling robust reading with error correction (i.e., mental processes and mathematical concepts).
Dependent claim 7 further recites:
each valid encoded alphabet letter πn of the sequence S = (π1, π2, …, πn…, πN-1, πN) belongs to a set of predefined alphabet letters
Σ
≡
σ
m
|
m
=
1
t
o
M
defined as binary occurrence vectors over the space spanned by said Z different types of short k-mer building blocks (i.e., mental processes and mathematical concepts).
Dependent claim 8 further recites:
said set of predefined alphabet letters
Σ
≡
σ
m
|
m
=
1
t
o
M
consists only of binary occurrence vectors of said space (i.e., mental processes and mathematical concepts); and
wherein at least one of the following:
said binary occurrence vectors are of equal weight (i.e., mental processes and mathematical concepts);
said binary occurrence vectors having hamming distances between them greater or equal to a certain second threshold H2 of minimal hamming distance wherein said second threshold H2 of minimal hamming distance is at least (H2≥2) (i.e., mental processes and mathematical concepts).
Dependent claim 13 further recites:
an identifying sequence…indicative of the population with which said molecular sequence is associated (i.e., mental processes); and
wherein said identifying sequence is different in molecular sequences associated with different ones of said one or more populations (i.e., mental processes).
Dependent claim 14 further recites:
the population identification section comprises an identifying sequence (i.e., mental processes);
a difference between the identifying sequences that are used in the population identification sections of different respective populations exceeds a predetermined threshold measured by a certain predetermined distance metric of strings, such as an edit or Hamming distance metric between strings (i.e., mental processes and mathematical concepts).
Dependent claim 21 further recites:
the Z different types of short k-mers in said building-block-set are characterized in that a hamming distance between each short k-mer in said building-block-set and any other short k-mer in said building-block-set is greater or equal to a certain first H1 threshold of minimal hamming distance, whereby said first threshold satisfies H1≥2 (i.e., mental processes and mathematical concepts); and
determining of the observed binary vector Xn of dimension Z associated with location n in the data encoding sections, comprises ignoring sequenced short k-mer found at said location in one or more of the data encoding sections which does not belong to the building block set (i.e., mental processes and mathematical concepts).
Dependent claim 22 further recites:
said predefined alphabet ∑ ≡ {σm}|m=1 to M consists only of binary vectors with hamming distances between them being greater or equal to a certain second threshold H2≥2 of minimal hamming distance, thereby providing that in case said match between the observed binary vector Xn and said vector of definition of one of the letters {σm}|m=1 to M of the alphabet ∑ is determined, said match being indicative of validity of the reading of the encoded letter πn from the locations n in said data encoding sections of sequenced molecular sequences (i.e., mental processes and mathematical concepts).
Dependent claim 24 further recites:
each letter X in the alphabet letters ∑ ≡ {σm}|m=1 to M is defined by occurrence of a predetermined exact number Y of the different types of short k-mers of said building-block-set {Ez}, said predetermined exact number Y being the same for all the encoded alphabet letters πn; and wherein a stopping condition of said sequencing is that per each location n of said 1 to N locations of the data encoding sections at least said exact number Y of different types of short k-mers belonging to said building-block-set {Ez} is found (i.e., mental processes and mathematical concepts);
Dependent claim 26 further recites:
each letter σm in the alphabet letters ∑ ≡ {σm}|m=1 to M, is defined by occurrence of a predetermined and constant exact number Y of the different types of short k-mers of said building-block-set {Ez}, said predetermined exact number Y being the same for all the alphabet letters (i.e., mental processes); and
a data reading validation/correction operation comprising selectively performing the following for each location n of said 1 to N locations of the data encoding sections at which a respective letter expected to be encoded:
(i) in case a weight Y' of said observed binary vector Xn is equal to said exact number Y, determining said encoded alphabet letters πn at the location n by mapping the observed binary vector Xn to one of the alphabet letters {σm}|m=1 to M based on a match between the observed binary vector Xn and a binary vector representation of said one alphabet letter (i.e., mental processes and mathematical concepts);
(ii) in case a weight Y' of said observed binary vector Xn is larger than said exact number Y, determining that an excess Y' - Y of different types of building blocks is found at the locations n of the data encoding sections; and computing statistical significances of each of the Y' different types of building blocks found at the location n based on a number of times each of said Y’ types of building blocks is sequenced from the locations n (i.e., mental processes and mathematical concepts), and:
in case statistical significance of Y' - Y types of said Y' building blocks are below a predetermined statistical significance threshold ST (i.e., mental processes and mathematical concepts), carrying out the following:
determining that said excess Y'- Y types of building blocks are the Y' - Y types of building blocks for which the statistical significance is below the threshold ST and amending said observed binary vector Xn accordingly to obtain an amended observed binary vector X’n of weight Y (i.e., mental processes and mathematical concepts); and
determining said encoded alphabet letters πn at the location n by mapping the amended observed binary vector X’n to one of the alphabet letters {σm}|m=1 to M based on a match between the amended observed binary vector X’n and a binary vector representation of said one alphabet letter (i.e., mental processes and mathematical concepts);
in case there are less than Y' - Y types of said Y’ building blocks whose statistical significances are below the predetermined statistical significance threshold ST, determining that the observed binary vector Xn may not be mapped to any one of the alphabet letters {σm}|m=1 to M and thereby the encoded alphabet letters πn at the location n is invalid (i.e., mental processes and mathematical concepts);
(iii) in case a weight Y' of said observed binary vector Xn is less than said exact number Y, determining that the observed binary vector Xn may not be mapped to any one of the alphabet letters {σm}|m=1 to M and thereby the encoded alphabet letters πn at the location n is invalid (i.e., mental processes and mathematical concepts).
Dependent claim 29 further recites:
each letter σm in the alphabet letters ∑ ≡ {σm}|m=1 to M is defined by occurrence of a predetermined exact number Y of the different types of short k-mers of said building-block-set {Ez}, said predetermined exact number Y being the same for all the alphabet letters (i.e., mental processes and mathematical concepts); and
a stopping condition of said sequencing is that per each location n of said 1 to N locations of the data encoding sections of at least said exact number Y of different types of short k-mers belonging to said building-block-set {Ez} is found (i.e., mental processes and mathematical concepts).
Dependent claim 30 further recites:
each letter σm in the alphabet letters ∑ ≡ {σm}|m=1 to M, is defined by occurrence of a predetermined exact number Y of the different types of short k-mers of said building-block-set {Ez}, said predetermined exact number Y being the same for all the alphabet letters (i.e., mental processes and mathematical concepts); and
carry out a data reading validation/correction operation according to the method of claim 26, as noted above (i.e., mental processes and mathematical concepts).
Dependent claim 32 further recites:
indicated to be occurring by the binary vector representing the letter πn (i.e., mental processes and mathematical concepts).
Dependent claim 33 further recites:
the first letter π1 being encoded (i.e., mental processes and mathematical concepts).
Dependent claim 41 further recites:
encoding data of a plurality of respective data blocks (i.e., mental processes and mathematical concepts).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., determining encoded alphabet letters πn of a sequence S = (π1, π2, …, πn…, πN-1, πN) encoded by said n = 1 to N locations by associating each observed binary vector Xn of each of said n = 1 to N locations, to one of alphabet letters {σm} of a predetermined alphabet ∑ ≡ {σm}|m=1 to M), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., the Z different types of short k-mers in said building-block-set are characterized in that a hamming distance between each short k-mer in said building-block-set and any other short k-mer in said building-block-set is greater or equal to a certain first H1 threshold of minimal hamming distance, whereby said first threshold satisfies H1≥2) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Dependent claims 2, 3, 5, 7, 8, 21, 22, and 26 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claim 1 include:
one or more populations of molecular sequences; and
each molecular sequence of the molecular sequences of the population comprises a data encoding section comprising a sequence of similar predetermined length N of short k-mers and have a similar predetermined size k≥2 (plurality) of bases.
The additional elements in independent claim 20 include:
providing a molecular data storage system comprising a population of molecular sequences; and
applying sequencing to the population of molecular sequences.
The additional elements in independent claim 27 include:
a sequencing control module configured and operable for connecting to a sequencing system for operating the sequencing system to perform the operations (i) and (ii) of claim 20 to thereby sequence a population of molecular sequences of the data storage system; and
a data inference processing module.
The additional elements in independent claim 31 include:
providing a support substrate having one or more spatially separated regions at which one or more respective populations of molecular sequences can be synthesized;
providing one or more blocks of data to be respectively encoded by the one or more respective populations of molecular sequences which are to be synthesized at said one or more spatially separated regions respectively;
synthesizing a corresponding population of molecular sequences at a respective region of said one or more regions; and
wherein said synthesizing of the population of molecular sequences at the respective region includes selectively depositing building blocks.
The additional elements in independent claim 36 include:
a container module comprising a plurality of containers;
a fabrication head fluidly connected to said Z containers and configured and operable for controlled deposition of basic molecular building-blocks contained in a one or more selected containers;
a control unit configured and operable to operate the fabrication head for implementing operations (b) and (c) of the method of claim 31; wherein said implementing comprises:
providing at least one block of data;
synthesizing the population of molecular sequences by operating said fabrication head; and
said fabrication head selectively deposits the molecular building blocks from said Z containers.
The additional elements in independent claim 45 include:
at least one population of molecular sequences; and
each molecular sequence of the molecular sequences of the population comprises a data encoding section comprising a sequence of similar predetermined length N of short k-mers and have a similar predetermined size k≥2 (plurality) of bases.
Dependent claims 13, 14, 17, 24, 29, 30, 32, 33, 35, 39, and 41 further recite the following additional elements, as noted below.
The additional element(s) in dependent claim 13 include(s):
each molecular sequence of the molecular sequences of the population includes a population identification section comprising a sequence of molecular bases indicative of the population with which said molecular sequence is associated.
The additional element(s) in dependent claim 14 include(s):
molecular bases included in said population identification section are bases of the same preselected set of bases by which said building-blocks are constructed.
The additional element(s) in dependent claim 17 include(s):
molecular sequences of one or more of said populations are contained together in a common region; and
the molecular sequences associated with the same population can be exclusively selected by utilizing binding molecules configured and operable for selectively binding to the population identification section of the molecular sequences associated with said same population.
The additional element(s) in dependent claim 24 include(s):
sequencing is carried out at least until said stopping condition is fulfilled or until a predetermined maximal sequencing depth.
The additional element(s) in dependent claim 29 include(s):
sequencing control module is adapted to operate the sequencing system at least until said stopping condition is fulfilled or until a predetermined maximal sequencing depth.
The additional element(s) in dependent claim 30 include(s):
data inference processing module.
The additional element(s) in dependent claim 32 include(s):
providing and placing molecular building blocks;
washing said region to remove un-bonded data encoding molecular building-blocks; and
applying un-blocking treatment to "un-block" the data encoding molecular building-blocks that are bounded to molecules at said region.
The additional element(s) in dependent claim 33 include(s):
the support substrate comprises cleavable molecules adapted to bind with said data encoding molecular building-blocks.
The additional element(s) in dependent claim 35 include(s):
synthesizing of the population of molecule sequences comprises synthesizing similar population identification segments, in all molecule sequences of said population.
The additional element(s) in dependent claim 39 include(s):
the fabrication head is configured and operable for depositing cleavable molecules at said region prior to said synthesizing; and
a harvesting module configured and operable for harvesting said population of molecules from said region by cleaving said cleavable molecules.
The additional element(s) in dependent claim 41 include(s):
said control unit is adapted for operating said fabrication head for synthesizing, for all molecules of said population, a similar identification section;
said control unit is configured and operable for operating said fabrication head to synthesize a plurality of population of molecular sequences.
The additional elements of one or more populations of molecular sequences and each molecular sequence of the molecular sequences of the population comprises a data encoding section comprising a sequence of similar predetermined length N of short k-mers and have a similar predetermined size k≥2 (plurality) of bases (claim 1); providing a molecular data storage system comprising a population of molecular sequences; and applying sequencing to the population of molecular sequences (claim 20); at least one population of molecular sequences (claim 45); each molecular sequence of the molecular sequences of the population comprises a data encoding section comprising a sequence of similar predetermined length N of short k-mers and have a similar predetermined size k≥2 (plurality) of bases (claim 45); sequencing is carried out at least until said stopping condition is fulfilled or until a predetermined maximal sequencing depth (claim 24); sequencing control module is adapted to operate the sequencing system at least until said stopping condition is fulfilled or until a predetermined maximal sequencing depth (claim 29); merely indicate a field of use or technological environment (i.e., molecular sequencing and/or synthesis) in which to apply a judicial exception (MPEP 2106.05(h)), and therefore do not meaningfully limit the claims because the claims do not recite any additional elements that are an improvement to computer functionality itself, or an improvement to another technology or technical field (i.e., molecular sequencing and/or synthesis), and thus the recited additional elements do not amount to more than a recitation of the words “apply it” (or an equivalent) and/or do not amount to more than mere instructions to implement an abstract idea (MPEP 2106.05(f)) by performing molecular sequencing and/or molecular synthesis, and therefore do not integrate the recited judicial exceptions into a practical application (MPEP 2106.04(d)).
The additional elements of a sequencing control module configured and operable for connecting to a sequencing system for operating the sequencing system to perform the operations (i) and (ii) of claim 20 to thereby sequence a population of molecular sequences of the data storage system; and a data inference processing module (claim 27); providing a support substrate having one or more spatially separated regions at which one or more respective populations of molecular sequences can be synthesized (claim 31); providing one or more blocks of data to be respectively encoded by the one or more respective populations of molecular sequences which are to be synthesized at said one or more spatially separated regions respectively; (claim 31); synthesizing a corresponding population of molecular sequences at a respective region of said one or more regions and wherein said synthesizing of the population of molecular sequences at the respective region includes selectively depositing building blocks (claim 31); a container module comprising a plurality of containers (claim 36); a fabrication head fluidly connected to said Z containers and configured and operable for controlled deposition of basic molecular building-blocks contained in a one or more selected containers (claim 36); a control unit configured and operable to operate the fabrication head for implementing operations (b) and (c) of the method of claim 31 (claim 36); molecular sequences of one or more of said populations are contained together in a common region (claim 17); the molecular sequences associated with the same population can be exclusively selected by utilizing binding molecules configured and operable for selectively binding to the population identification section of the molecular sequences associated with said same population (claim 17); data inference processing module (claim 30); synthesizing of the population of molecule sequences comprises synthesizing similar population identification segments, in all molecule sequences of said population (claim 35); the fabrication head is configured and operable for depositing cleavable molecules at said region prior to said synthesizing (claim 39); a harvesting module configured and operable for harvesting said population of molecules from said region by cleaving said cleavable molecules (claim 39); said control unit is adapted for operating said fabrication head for synthesizing, for all molecules of said population, a similar identification section (claim 41); and said control unit is configured and operable for operating said fabrication head to synthesize a plurality of population of molecular sequences (claim 41); merely indicate a field of use or technological environment (i.e., molecular sequencing and/or synthesis) in which to apply a judicial exception (MPEP 2106.05(h)), and therefore do not meaningfully limit the claims because the claims do not recite any additional elements that are an improvement to computer functionality itself, or an improvement to another technology or technical field (i.e., molecular sequencing and/or synthesis), and thus the recited additional elements do not amount to more than a recitation of the words “apply it” (or an equivalent) and/or do not amount to more than mere instructions to implement an abstract idea (MPEP 2106.05(f)) by performing molecular sequencing and/or molecular synthesis, and therefore do not integrate the recited judicial exceptions into a practical application (MPEP 2106.04(d)).
The additional elements of each molecular sequence of the molecular sequences of the population includes a population identification section comprising a sequence of molecular bases indicative of the population with which said molecular sequence is associated (claim 13); molecular bases included in said population identification section are bases of the same preselected set of bases by which said building-blocks are constructed (claim 14); providing and placing molecular building blocks (claim 32); washing said region to remove un-bonded data encoding molecular building-blocks (claim 32); applying un-blocking treatment to "un-block" the data encoding molecular building-blocks that are bounded to molecules at said region (claim 32); the support substrate comprises cleavable molecules adapted to bind with said data encoding molecular building-blocks (claim 33); merely indicate a field of use or technological environment (i.e., molecular sequencing and/or synthesis) in which to apply a judicial exception (MPEP 2106.05(h)), and therefore do not meaningfully limit the claims because the claims do not recite any additional elements that are an improvement to computer functionality itself, or an improvement to another technology or technical field (i.e., molecular sequencing and/or synthesis), and thus the recited additional elements do not amount to more than a recitation of the words “apply it” (or an equivalent) and/or do not amount to more than mere instructions to implement an abstract idea (MPEP 2106.05(f)) by performing molecular sequencing and/or molecular synthesis, and therefore do not integrate the recited judicial exceptions into a practical application (MPEP 2106.04(d)).
Thus, the additionally recited elements do not amount to an improvement do not amount to more than mere instructions to implement an abstract idea and/or do not amount to more than a field of use in which to apply a judicial exception; and as such, when all limitations in claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Dependent claims 2, 3, 5, 7, 8, 21, 22, and 26 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claims 1, 20, 27, 31, 36, and 45 and dependent claims 13, 14, 17, 24, 29, 30, 32, 33, 35, 39, and 41 are identified above, and carried over from Step 2A Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional elements identified at Eligibility Step 2A Prong Two and discussed above are conventional additional elements.
Evidence of the conventionality is shown be Ceze et al. (“Molecular digital data storage using DNA.” Nature, 2019, Vol. 20, pp. 456-466, as cited in the Information Disclosure Statement (IDS) received 12 July 2022). Ceze et al. reviews molecular digital data storage using DNA (Title; and Abstract) and shows that the basic process in DNA storage involves encoding digital information into DNA sequences (encoding), writing the sequences into actual DNA molecules (synthesis), physically conditioning and organizing then into a library for long-term storage, retrieving and selectively accessing them (random access), reading the molecules (sequencing) and converting them back to digital data (decoding) (page 456, col. 2, para. 3). Ceze et al. further shows an overview of the major steps of digital data storage in DNA (Figure 2) where first, a computer algorithm maps strings of bits into DNA sequences which are then machine synthesized (write), thereby generating many physical copies of each sequence. Solid-phase synthesis via phosphoramidite-based chemical synthesis can be done on a column (low-throughput) or array (high-throughput) solid support. After synthesis, the resulting DNA material can be cloned and stored within a biological cell (in vivo) or, more commonly, stored in vitro, such as being frozen in solution or dried down for protection from the environment (store). DNA data requested to be read can be selectively retrieved from the DNA pool in a process called random access (retrieve), where random access within DNA data pools can be accomplished with PCR-based enrichment with primer pairs that map to specific data items generated during the encoding process. Finally, automated sequencing instruments are used to generate a set of reads that correspond to the molecules they can detect (read), with the most common sequencing methods being Sanger (low-throughput) and sequencing-by-synthesis instruments (high-throughput, e.g., by Illumina), and more recently, nanopore sequencing (e.g., from Oxford Nanopore Technologies (ONT)) has been used for real-time data reading. Ceze et al. further reviews DNA synthesis technology, e.g., phosphoramidite-based oligonucleotide synthesis for writing DNA (page 461, col. 2, para. 2); array-based synthesis enabling the synthesis of different sequences in different spots in a solid substrate (page 461, col. 2, para. 3); and enzymatic synthesis for writing DNA (page 461, col. 2, para. 5 and page 462, col. 1). Ceze et al. further reviews DNA sequencing technologies for data retrieval (page 462, col. 1 and col. 2) including nanopore sequencing technology enabling real-time sequencing.
Therefore, when taken alone, all additional elements in claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) 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, 3, 7, 13, 14, 17, 20, 35, and 45 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Anavy et al. (“Data storage in DNA with fewer synthesis cycles using composite DNA letters.” Nature Biotechnology. October 2019, Vol. 37, pp. 1229-1236, as cited in the Information Disclosure Statement (IDS) received 12 July 2022).
Regarding claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45, Anavy et al. shows a molecular implementation of a storage system based on a composite alphabet (page 1230, col. 2, para. 4) (claims 1 and 20); a composite DNA letter is a representation of a position in a sequence that consists of a mixture of all four DNA nucleotides in a predetermined ratio and simulating encoding with larger composite alphabets (Abstract) (claims 1 and 20); an encoded DNA pool consisting of oligonucleotides having the same length (page 1230, col. 2, para. 4) (claims 1, 2, and 20); the payload was translated to a six-letter composite DNA alphabet in 5-bit chunks that comprise 2 nucleotides (i.e., less than 20 bases) (Figure 2(i) text and upper right corner of Figure) (claim 3); the steps of the decoding process show preprocessing and grouping by prefix symbol (Figure 3(a)) (claims 14 and 17); the decoding process uses an inference step at a single synthesized composite position, with the observed frequencies used to infer the source as the closest composite letter (Figure 1(c)) (claims 1 and 20); inference of the original letter is performed by converting the readout to a vector of base frequencies and comparing it to the base frequencies of the candidate letters in the composite alphabet (page 1230, col. 2, para. 3) (claims 7 and 20); experiment identifier and amplification template sequences were appended to each valid sequence (Figure 2, step (iv)) (claims 13, 14, and 35); inserting the encoded composite DNA sequence into a synthetic construct containing amplification primer templates, a unique molecular identifier and a barcode (Methods, page 2, col. 1, bottom) (claim 45); and to read a message coded using composite DNA letters correctly, the original message must be inferred from the observed reads in sufficiently many positions of the total message, where the sequencing readout (that is, the observed sequencing reads) is the product of a complex process, consisting of DNA synthesis, long-term storage, sampling and DNA sequencing (page 1230, col. 1, bottom) (claim 20).
Therefore, Anavy et al. anticipates claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 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, 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 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 5, 8, 21, 22, 24, 27, 29, 31, 32, 33, 36, 39, and 41 are rejected under 35 U.S.C. 103 as being unpatentable over Anavy et al. (“Data storage in DNA with fewer synthesis cycles using composite DNA letters.” Nature Biotechnology. October 2019, Vol. 37, pp. 1229-1236, as cited in the Information Disclosure Statement (IDS) received 12 July 2022) as applied to claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45 under 35 U.S.C. 102 above, and further in view of Takahashi et al. (“Demonstration of End-to-End Automation of DNA Data Storage.” Scientific Reports, 2019, Vol. 9:4998, pp. 1-5).
Anavy et al. as applied to claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45 under 35 U.S.C. 102 above, does not show reading with error correction using hamming distance analysis (claims 5, 8, 21, and 22); sequencing is carried out at least until said stopping condition is fulfilled or until a predetermined maximal sequencing depth (claim 24); a sequencing control module and a data inference control module (claim 27); said sequencing control module is adapted to operate the sequencing system at least until said stopping condition is fulfilled or until a predetermined maximal sequencing depth (claim 29); providing a support substrate having one or more spatially separated regions at which one or more respective populations of molecular sequences can be synthesized (claim 31); synthesizing a corresponding population of molecular sequences at a respective region of said one or more regions by selectively depositing molecules (claim 31); depositing comprises providing and placing molecules at said respective region to thereby enable their binding to molecules at said region (claim 32); said region of the support substrate comprises cleavable molecules adapted for binding to molecules such that deposition of the basic molecules are bounded to said cleavable molecules enabling harvesting said population of molecules from said respective region by cleaving said cleavable molecules (claim 33); a container module comprising a plurality of containers (claim 36); a fabrication head fluidly connected to said Z containers and configured and operable for controlled deposition of basic molecules (claim 36); a control unit configured and operable to operate the fabrication head (claim 36); providing data to be encoded by synthesizing a respective population of molecular sequences encoding said data (claim 36); the fabrication head is configured and operable for depositing cleavable molecules at said region prior to said synthesizing (claim 39); a harvesting module configured and operable for harvesting said population of molecules from said region by cleaving said cleavable molecules (claim 39); said control unit is adapted for operating said fabrication head for synthesizing, for all molecules of said population, a similar identification section (claim 41); or said control unit is configured and operable for operating said fabrication head to synthesize a plurality of population of molecular sequences at different spatially separated respective regions (claim 41).
Takahashi et al. shows a device that encodes data into a DNA sequence, which is then written to a DNA oligonucleotide using a DNA synthesizer, then the DNA is pooled for liquid storage, and later read using a nanopore sequencer (Abstract).
Regarding claims 5, 8, 21, and 22, Takahashi et al. further shows that once sequencing begins, a decode software module aligns each read and if the read is a valid read, the decoder attempts to error check/correct the payload using a Hamming code with an additional parity bit for correcting single-base errors and detecting a double-base errors (page 2, bottom).
Regarding claim 24, Takahashi et al. further shows nanopore sequencing using an Oxford Nanopore Technologies MinION (i.e., the MinION features include real-time selective sequencing) (page 4, middle).
Regarding claims 27, 29, and 30, Takahashi et al. further shows a DNA data storage system comprising an encode/decode software module, a DNA synthesis module, and a DNA preparation and sequencing module (page 1, para. 3; and Fig. 1(b) and (c)).
Regarding claims 31, 32, 33, 36, 39, and 41, Takahashi et al. further shows DNA synthesis using a BioAutomation synthesis column (i.e., a solid support) (page 4, paras. 2-4; and Fig. 1(b), (c), and (d)).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method shown by Anavy et al. as applied to claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45 under 35 U.S.C. 102 above, by incorporating data analysis methods for error correction of sequencing reads, as well as incorporating the hardware for synthesizing molecules and sequencing molecules, as shown by Takahashi et al., and discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Anavy et al. as applied to claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45 under 35 U.S.C. 102 above, with the methods of Takahashi et al., because Takahashi et al. shows methods and equipment for synthesizing and sequencing molecules, and particularly in the technical area of encoding digital data for DNA storage and the subsequent step of decoding. This modification would have had a reasonable expectation of success given that both Anavy et al. as applied to claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45 under 35 U.S.C. 102 above, and Takahashi et al. disclose methods for encoding and decoding digital data for storage using DNA molecules.
Claims 26 and 30 rejected under 35 U.S.C. 103 as being unpatentable over Anavy et al. (“Data storage in DNA with fewer synthesis cycles using composite DNA letters.” Nature Biotechnology. October 2019, Vol. 37, pp. 1229-1236, as cited in the Information Disclosure Statement (IDS) received 12 July 2022, and as cited above).
Anavy et al. as applied to claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45 under 35 U.S.C. 102 above, does not explicitly show the data encoding steps (claim 26) or using a data inference processing module (claim 30).
Regarding claims 26 and 30, Anavy et al. shows a method for data storage in DNA using composite letters (i.e., a composite alphabet) to increase the logical density of DNA storage above the strict, single-molecule, theoretical limit of 2 bits per synthesis cycle, and further shows using composite letters to form the basis of a DNA synthesis approach that trades sequence multiplicity for increased complexity of the synthesized DNA, effectively extending the available alphabet and therefore allowing higher data content per synthesis cycle, and further shows related methods including error-correction codes (page 1229, col. 2, para. 1; and throughout).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method shown by Anavy et al. as applied to claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45 under 35 U.S.C. 102 above, by incorporating the methods comprising operations for data reading validation/correction. One of ordinary skill in the art would have been motivated to modify Anavy et al. as applied to claims 1, 2, 3, 7, 13, 14, 17, 20, 35, and 45 under 35 U.S.C. 102 above, because Anavy et al. shows that using a composite alphabet extends the available alphabet allowing for higher data content per synthesis cycle, but also involves tradeoffs including the need for error-correction. This modification would have had a reasonable expectation of success given that Anavy et al. is directed to data storge in DNA with fewer synthesis cycles using composite letters.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
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 reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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.
Claims 1-3, 5, 7, 8, 13, 14, 17, 20-22, 24, 26, 27, 29-33, 35, 36, 39, 41, and 45 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of U.S. Patent No. 12,443,366. Although the claims at issue are not identical, they are not patentably distinct from each other because the methods and systems of the instant application are drawn to the same methods and systems of the ‘366 patent of using letters of a composite alphabet to encode and decode data for storage and retrieval, respectively, using DNA molecules.
Instant independent claim 1 and claims dependent therefrom recite substantially the same limitations as independent claim 1 and those claims dependent therefrom in the ‘366 patent.
Instant independent claim 20 and claims dependent therefrom recite substantially the same limitations as independent claim 16 and those claims dependent therefrom in the ‘366 patent.
Instant independent claim 27 and claims dependent therefrom recite substantially the same limitations as independent claim 20 and those claims dependent therefrom in the ‘366 patent.
Instant independent claim 45 recites substantially the same limitations as independent claim 14 and those claims dependent therefrom in the ‘366 patent.
Conclusion
No claims are allowed.
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this application.
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687