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 1-19 are currently pending and under exam herein.
Claims 1-19 are rejected.
Priority
The instant application claims priority from foreign application KR10-2020-0110636 filed on 8/31/2020 and is a 371 of PCT/KR2021/011635 filed on 8/31/2021. Thus, the earliest effective filing date of the instant application is 8/31/2020.
Drawings
The Drawings filed on 2/16/2023 were considered.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 2/16/2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
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 1-19 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: Claims 1-18 are directed to a computer-implemented method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest. Claim 19 is directed to a computer readable storage medium which is ineligible. Examiner will assume non-transitory computer readable storage medium for the purpose of compact prosecution.
[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:
(a) receiving a name of the target nucleic acid molecule and a name of the organism of interest and retrieving synonyms for the target nucleic acid molecule of the organism of interest; (mathematical concept)
(b) retrieving nucleic acid sequence data included in nucleic acid records, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule and the retrieved synonyms are described; (mathematical concept)
(c) sorting the retrieved nucleic acid data according to taxonomic name and/or taxonomic identification (ID) and selecting taxonomic representative sequences among nucleic acid sequence data having the same taxonomic name and/or taxonomic ID; (mathematical concept/ mental process)
(d) grouping the selected taxonomic representative sequences according to homology and selecting a group representative sequence for each group (mathematical concept/ mental process)
(e) retrieving nucleic acid sequence data having a homology of a predetermined value or more with the group representative sequence to provide the retrieved nucleic acid sequence data as a nucleic acid sequence data set for the design of an oligonucleotide (mathematical concept/ mental process)
Dependent claim 2 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein in step (a), the name of the target nucleic acid molecule, a name of a protein encoded by the target nucleic acid molecule, and a name of an organism are received and the synonyms for the target nucleic acid molecule and the protein of the organism are retrieved (mathematical concept)
Dependent claim 3 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the nucleic acid sequence data in step (b) include nucleic acid sequence data corresponding to a part or the entirety of the target nucleic acid molecule or variant nucleic acid sequence data for the target nucleic acid molecule. (mathematical concept)
Dependent claim 4 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the retrieving of nucleic acid sequence data in the step (b) is performed by the method comprising the following steps: (b-1) retrieving identifiers of nucleic acid records, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule and the retrieved synonyms are described; (mathematical concept)
and (b-2) retrieving nucleic acid sequence data specified by the identifiers (mathematical concept)
Dependent claim 5 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein in step (b-1), the identifiers of the nucleic acid records are retrieved, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule, a name of a protein, and the retrieved synonyms are described (mathematical concept)
Dependent claim 6 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein in step (b-2), nucleic acid sequence data corresponding to the target nucleic acid molecule are selectively retrieved in the nucleic acid sequence data specified by the identifiers (mathematical concept)
Dependent claim 7 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein step (b-2) includes the following steps: (b-2-1) retrieving nucleic acid records specified by the identifiers; and (mathematical concept)
(b-2-2) retrieving nucleic acid sequence data corresponding to the target nucleic acid molecule from the nucleic acid records (mathematical concept)
Dependent claim 8 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein in step (b-2-2), the nucleic acid sequence data corresponding to the target nucleic acid molecule and identification information of the nucleic acid sequence data are selectively retrieved from the nucleic acid records, wherein the selective retrieving of the nucleic acid sequence data and the identification information of the nucleic acid sequence data includes the following steps: (b-2-2-1) determining, as a valid sub-record, a sub-record in which the synonym is recorded in a first specification that is predetermined, among one or more sub-records in each of the nucleic acid records (mathematical concept)
(b-2-2-2) determining, as a valid sub-record, a sub-record in which the synonym is recorded in a second specification, when there is no valid sub- record determined by the first specification in the nucleic acid record (mathematical concept)
(b-2-2-3) determining, as a valid sub-record, a sub-record in which the synonym is recorded in a third specification, when there is no valid sub-record determined by the second specification in the nucleic acid record; and (mathematical concept)
(b-2-2-4) retrieving nucleic acid sequence data corresponding to the determined valid sub-record and identification information thereof. (mathematical concept)
Dependent claim 9 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the method further comprises, between steps (b) and (c), the following steps: (b-3) sorting the retrieved nucleic acid sequence data according to the biosample identification to select nucleic acid sequence data having the same biosample identification; (mathematical concept)
(b-4) sorting the selected nucleic acid sequence data so as to satisfy at least one of the following sort criteria; (b-5) selecting a nucleic acid sequence of the highest-ranked nucleic acid sequence data among the sorted nucleic acid sequence data; and (mathematical concept)
(b-6) deleting nucleic acid sequence data except for the highest-ranked nucleic acid sequence data from the retrieved nucleic acid sequence data, wherein the sort criteria include the following: (i) sorting the selected nucleic acid sequence data according to the assembly level, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order; and (mathematical concept)
(ii) sorting the selected nucleic acid sequence data according to whether the selected nucleic acid sequence data are included in a reference sequence (RefSeq) database, wherein the ranking is higher when the nucleic acid sequence data are included in the RefSeq database than when not included (mathematical concept)
Dependent claim 10 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the selecting of the taxonomic representative sequence in step (c) is performed by a method including the following steps: (c-1) sorting the nucleic acid sequence data having the same taxonomic name and/or taxonomic ID so as to satisfy at least one of the following predetermined sort criteria; and (mathematical concept)
(c-2) selecting, as the taxonomic representative sequence, a nucleic acid sequence of the highest-ranked nucleic acid sequence data among the sorted nucleic acid sequence data, wherein the predetermined sort criteria include the following: (mathematical concept)
(i) sorting according to the assembly level of the nucleic acid sequence data, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order; (mathematical concept)
(ii) sorting according to whether the nucleic acid sequence data are included in a reference sequence (RefSeq) database, wherein the ranking is higher when the nucleic acid sequence data are included in the RefSeq database than when not included; (mathematical concept)
(iii) sorting according to whether a name of a nucleic acid molecule described in a descriptor of a nucleic acid record containing the nucleic acid sequence data is identical to at least one of the received name of the target nucleic acid and the retrieved synonyms, wherein the ranking is higher when identical than when not identical; (mathematical concept)
(iv) sorting according to the length of the nucleic acid sequence data, wherein the longer the length, the higher the ranking; (mathematical concept)
(v) sorting according to whether there is description in a host of a descriptor of a nucleic acid record containing the nucleic acid sequence data, wherein the ranking is higher when a host of interest for the organism of interest is described in the host than when not described, and higher when an organism different from the organism of interest are not described in the host than when described; (mathematical concept)
(vi) sorting according to the registration date or revision date of a nucleic acid record containing the nucleic acid sequence data, wherein the more recent the registration date or revision date, the higher the ranking; and (mathematical concept)
(vii) sorting according to the alphabetical order in accession number of the nucleic acid sequence data, wherein the earlier the alphabetical order of the accession number, the higher the ranking. (mathematical concept)
Dependent claim 11 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the selecting of the group representative sequence in step (d) is performed by a method including the following steps: (d-1) sorting the selected taxonomic representative sequences so as to satisfy at least one of the following predetermined sort criteria; (mathematical concept)
(d-2) selecting the highest-ranked taxonomic representative sequence among the sorted taxonomic representative sequences; and (mathematical concept)
(d-3) grouping taxonomic representative sequences having a homology of a predetermined value or more with the highest-ranked taxonomic representative sequence and selecting the highest-ranked taxonomic representative sequence as the group representative sequence in each group, wherein the sort criteria include the following: (mathematical concept)
(i) sorting according to the assembly level of the selected taxonomic representative sequence, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order; (mathematical concept)
(ii) the number of nucleic acid sequence data having the same taxonomic name and/or taxonomic ID as the selected taxonomic representative sequence, wherein the larger the number, the higher the ranking; (mathematical concept)
(iii) sorting according to whether there is a description in a host of a descriptor of a nucleic acid record containing the selected taxonomic representative sequence, wherein the ranking is higher when a host of interest for the organism of interest is described in the host than when not described, and higher when an organism different from the host of interest is not described in the host than when described; and (mathematical concept)
(iv) sorting according to the alphabetic order of accession number in the selected taxonomic representative sequence, wherein the earlier the alphabetic order of the accession number, the higher the ranking. (mathematical concept)
Dependent claim 12 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the method further comprises step (f) of providing, as a target nucleic acid sequence data set for the target nucleic acid molecule, nucleic acid sequence data associated with the received organism of interest in the nucleic acid sequence data set provided in step (e). (mathematical concept)
Dependent claim 13 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the target nucleic acid sequence data set provided in step (f) has a homology of a predetermined value or more with at least one representative sequence of the group representative sequences and the taxonomic representative sequences for the target nucleic acid sequence data set (mathematical concept)
Dependent claim 14 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the method further comprises step (g) of providing, as a non-target nucleic acid sequence data set for a non-target nucleic acid molecule, nucleic acid sequence data not associated with the received organism of interest from the nucleic acid sequence data set provided in step (e) (mathematical concept)
Dependent claim 15 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the non-target nucleic acid sequence data set provided in step (g) satisfies at least one of the following homology criteria: (i) the non-target nucleic acid sequence data set needs to have a homology of a predetermined value or more with a partial sequence region of at least one representative sequence of the group representative sequence and the taxonomic representative sequence; (ii) the non-target nucleic acid sequence data set needs to have a homology of a predetermined value or more with at least one representative sequence of the group representative sequence and the taxonomic representative sequence; and (iii) the non-target nucleic acid sequence data set having homology criterion (i) needs to have homology criterion (ii) (mathematical concept)
Dependent claim 16 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the method further comprises the following steps: (h) retrieving nucleic acid sequence data having a homology of a predetermined value or more with the group representative sequence to provide a nucleic acid sequence data set; and (mathematical concept)
(j) classifying, as design exclusion target nucleic acid sequence data, target nucleic acid sequence data of the group representative sequence and target nucleic acid sequence data belonging to the same group as the group representative sequence in the target nucleic acid sequence data set in step (f), when the taxonomic name and/or taxonomic ID of the organism associated with the group representative sequence satisfies one of the following predetermined criteria, wherein the predetermined criteria include the following: (i) nucleic acid sequence data corresponding to the taxonomic name and/or taxonomic ID of the organism associated with the group representative sequence are absent and only nucleic acid sequence data corresponding to a taxonomic name and/or taxonomic ID of an organism different from the organism associated with the group representative sequence are present in the nucleic acid sequence data set provided in step (h); (mathematical concept)
(ii) the homology of nucleic acid sequence data corresponding to the taxonomic name and/or taxonomic ID of the organism associated with the group representative sequence is lower than the homology of nucleic acid sequence data corresponding to a taxonomic name and/or taxonomic ID of an organism different from the organism associated with the group representative sequence, in the nucleic acid sequence data set provided in step (h); (mathematical concept)
(iii) target nucleic acid sequence data corresponding to the taxonomic name and/or taxonomic ID of the organism associated with the group representative sequence are absent in the nucleic acid sequence data set provided in step (h), and the proportion of nucleic acid sequence data of an organism corresponding to a superclass taxonomic name and/or taxonomic ID of the organism associated with the group representative sequence or a subclass taxonomic name and/or taxonomic ID of the superclass is less than a predetermined value relative to the nucleic acid sequence data set provided in step (h); and (mathematical concept)
(iv) all of the nucleic acid sequence data set provided in step (h) is associated with a nucleic acid sequence data set of the organism associated with the group representative sequence, but a name of a target nucleic acid molecule described in a descriptor of each of nucleic acid records containing the nucleic acid sequence data set is absent or different from at least one of the name of the target nucleic acid molecule and the retrieved synonyms. (mathematical concept)
Dependent claim 17 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the method further comprises, after step (e), the following steps: (e-1) sorting the provided nucleic acid sequence data set for the design according to the biosample identification to select nucleic acid sequence data having same biosample identification; (mathematical concept)
(e-2) sorting the selected nucleic acid sequence data so as to satisfy at least one of the following sort criteria; (mathematical concept)
(e-3) selecting a nucleic acid sequence of the highest-ranked nucleic acid sequence data among the sorted nucleic acid sequence data; and (mathematical concept)
(e-4) deleting nucleic acid sequence data except for the highest-ranked nucleic acid sequence data from the nucleic acid sequence data set for the design, wherein the sort criteria include the following: (i) sorting nucleic acid sequences included in the provided nucleic acid sequence data set for the design according to the assembly level, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order; and (mathematical concept)
(ii) sorting whether nucleic acid sequences included in the provided nucleic acid sequence data set for the design are included in a reference sequence (RefSeq) database, wherein the ranking is higher when the nucleic acid sequence data are included in the RefSeq database than when not included. (mathematical concept)
Dependent claim 18 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
wherein the method further comprises the following steps: (k) retrieving nucleic acid sequence data having a homology of a predetermined value or more with the non-target nucleic acid sequence of the organism associated with the non-target nucleic acid sequence data set to provide a nucleic acid sequence data set; and (mathematical concept)
(1) classifying, as design exclusion non-target nucleic acid sequence data, non-target nucleic acid sequence data of the organism in the non-target nucleic acid sequence data set in step (k), when the taxonomic name and/or taxonomic ID of the organism associated with the non-target nucleic acid sequence satisfies one criterion of the following predetermined criteria, wherein the predetermined criteria include the following: (mathematical concept)
(i) nucleic acid sequence data corresponding to the taxonomic name and/or taxonomic ID of the organism associated with the non-target nucleic acid sequence are absent and only nucleic acid sequence data corresponding to a taxonomic name and/or taxonomic ID of an organism different from the organism are present in the nucleic acid sequence data set provided in step (k); (mathematical concept)
(ii) the homology of the non-target nucleic acid sequence data corresponding to the taxonomic name and/or taxonomic ID of the organism associated with the non-target nucleic acid sequence is lower than the homology of nucleic acid data corresponding to a taxonomic name and/or taxonomic ID of an organism different from the organism in the nucleic acid sequence data set provided in step (k); and (mathematical concept)
(iii) non-target nucleic acid sequence data corresponding to the taxonomic name and/or taxonomic ID of the organism associated with the non-target nucleic acid sequence are absent in the nucleic acid sequence data set provided in step (k), and the proportion of nucleic acid sequence data of an organism corresponding to a superclass taxonomic name and/or taxonomic ID of the organism or a subclass taxonomic name and/or taxonomic ID of the superclass is less than a predetermined value relative to the nucleic acid sequence data set provided in step (k) (mathematical concept)
Independent claim 19 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
(a) receiving a name of the target nucleic acid molecule and a name of the organism of interest and retrieving synonyms for the target nucleic acid molecule of the organism of interest; (mathematical concept)
(b) retrieving nucleic acid sequence data included in nucleic acid records, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule and the retrieved synonyms are described (mathematical concept)
(c) sorting the retrieved nucleic acid data according to taxonomic name and/or taxonomic identification (ID) and selecting taxonomic representative sequences among nucleic acid sequence data having the same taxonomic name and/or taxonomic ID; (d) grouping the selected taxonomic representative sequences according to homology and selecting a group representative sequence for each group; and (mathematical concept/ mental process)
(e) retrieving nucleic acid sequence data having a homology of a predetermined value or more with the group representative sequence to provide the retrieved nucleic acid sequence data as a nucleic acid sequence data set for the design of an oligonucleotide. (mathematical concept/ mental process)
Organizing information and manipulating information through mathematical correlations, Digitech Image Techs., LLC v. Electronics for Imaging, Inc., 758 F.3d 1344, 1350, 111 USPQ2d 1717, 1721 (Fed. Cir. 2014). The patentee in Digitech claimed methods of generating first and second data by taking existing information, manipulating the data using mathematical functions, and organizing this information into a new form. The court explained that such claims were directed to an abstract idea because they described a process of organizing information through mathematical correlations, like Flook's method of calculating using a mathematical formula. 758 F.3d at 1350, 111 USPQ2d at 1721 and a claim to "collecting information, analyzing it, and displaying certain results of the collection and analysis," where the data analysis steps are recited at a high level of generality such that they could practically be performed in the human mind, Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016);
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 pencil and paper, 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 are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 1-19 recite an abstract idea as the dependent claims will inherit the abstract ideas from the independent claims.
[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.
The additional element in independent claim 1 includes:
A computer-implemented method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising
The additional element in independent claim 19 includes:
A computer readable storage medium containing instructions to configure a processor to perform a method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising:
The additional elements of are insignificant extra-solution activity that are a computer-implemented method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising (Claim 1), A computer readable storage medium containing instructions to configure a processor to perform a method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising (Claim 19) fail to integrate a judicial exception into a practical application merely reciting the words "apply it" (or an equivalent) with the judicial exception, or merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f).
Claims 2-18 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
Thus, the additionally recited elements merely invoke a computer as a tool, and/or amount to insignificant extra-solution data gathering activity, and as such, when all limitations in claims 1-19 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 1-19 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.
The additional elements recited in claims 1, 19 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 of are insignificant extra-solution activity that are a computer-implemented method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising (Claim 1), A computer readable storage medium containing instructions to configure a processor to perform a method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising (Claim 19) fail to integrate a judicial exception into a practical application merely reciting the words "apply it" (or an equivalent) with the judicial exception, or merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f).
Claims 1-19 do not recite any elements in addition to the judicial exception. Therefore, when taken alone, all additional elements in claims 1-19 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 1-19 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 § 103
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 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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 1-11, 13, 15, 19 are rejected under 35 U.S.C. 103 as being unpatentable over Malgott et al. (Maglott, D. Entrez Gene: Gene-Centered Information at NCBI. Nucleic Acids Research 2004, 33 (Database issue), D54–D58.) in view of Sayers (Sayers, E. A General Introduction to the E-utilities. (2009)) in further view of Kitts et al. (Kitts et al. Assembly: A Resource for Assembled Genomes at NCBI. Nucleic Acids Research 2015, 44 (D1), D73–D80.) in further view of Li et al. (Li, W.; Godzik, A. Cd-Hit: A Fast Program for Clustering and Comparing Large Sets of Protein or Nucleotide Sequences. Bioinformatics 2006, 22 (13), 1658–1659.) in further view of Camacho et al. (Camacho et al. BLAST+: Architecture and Applications. BMC Bioinformatics 2009, 10 (1), 421.) in further view of O’Leary et al. (O’Leary et al. Reference Sequence (RefSeq) Database at NCBI: Current Status, Taxonomic Expansion, and Functional Annotation. Nucleic Acids Research 2015, 44 (D1), D733–D745.). The italicized text corresponds to the instant claim limitations.
With respect to the limitations of Claims 1, 2, 5, 8, 19, Malgott et al. teaches a GUI that intakes a gene name and an organism and output expands that name into aliases so more records can be found. The summary includes the species of origin, preferred and alternate (Other aliases) symbols, preferred and other (Other designations) descriptive names, chromosome localization, the Gene ID. NCBI Gene stores protein designation alongside gene aliases. (pg. D55 Figure 1 Caption, (a) receiving a name of the target nucleic acid molecule and a name of the organism of interest and retrieving synonyms for the target nucleic acid molecule of the organism of interest (Claim 1), wherein in step (a), the name of the target nucleic acid molecule, a name of a protein encoded by the target nucleic acid molecule, and a name of an organism are received and the synonyms for the target nucleic acid molecule and the protein of the organism are retrieved (Claim 2), wherein in step (b-1), the identifiers of the nucleic acid records are retrieved, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule, a name of a protein, and the retrieved synonyms are described (Claim 5), (b-2-2-2) determining, as a valid sub-record, a sub-record in which the synonym is recorded in a second specification, when there is no valid sub- record determined by the first specification in the nucleic acid record; (b-2-2-3) determining, as a valid sub-record, a sub-record in which the synonym is recorded in a third specification, when there is no valid sub-record determined by the second specification in the nucleic acid record; (Claim 8), (a) receiving a name of the target nucleic acid molecule and a name of the organism of interest and retrieving synonyms for the target nucleic acid molecule of the organism of interest (Claim 19)
Malgott et al. does not explicitly teach
A computer-implemented method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising (Claim 1)
(e) retrieving nucleic acid sequence data having a homology of a predetermined value or more with the group representative sequence to provide the retrieved nucleic acid sequence data as a nucleic acid sequence data set for the design of an oligonucleotide (Claim 1)
(d) grouping the selected taxonomic representative sequences according to homology and selecting a group representative sequence for each group; and (Claim 1)
(c) sorting the retrieved nucleic acid data according to taxonomic name and/or taxonomic identification (ID) and selecting taxonomic representative sequences among nucleic acid sequence data having the same taxonomic name and/or taxonomic ID (Claim 1)
(b) retrieving nucleic acid sequence data included in nucleic acid records, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule and the retrieved synonyms are described (Claim 1)
wherein the nucleic acid sequence data in step (b) include nucleic acid sequence data corresponding to a part or the entirety of the target nucleic acid molecule or variant nucleic acid sequence data for the target nucleic acid molecule (Claim 3)
wherein the retrieving of nucleic acid sequence data in the step (b) is performed by the method comprising the following steps: (b-1) retrieving identifiers of nucleic acid records, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule and the retrieved synonyms are described; and (b-2) retrieving nucleic acid sequence data specified by the identifiers (Claim 4)
nucleic acid sequence data corresponding to the target nucleic acid molecule are selectively retrieved in the nucleic acid sequence data specified by the identifiers (Claim 6)
wherein step (b-2) includes the following steps: (b-2-1) retrieving nucleic acid records specified by the identifiers; and (b-2-2) retrieving nucleic acid sequence data corresponding to the target nucleic acid molecule from the nucleic acid records (Claim 7)
wherein in step (b-2-2), the nucleic acid sequence data corresponding to the target nucleic acid molecule and identification information of the nucleic acid sequence data are selectively retrieved from the nucleic acid records, wherein the selective retrieving of the nucleic acid sequence data and the identification information of the nucleic acid sequence data includes the following steps: (b-2-2-1) determining, as a valid sub-record, a sub-record in which the synonym is recorded in a first specification that is predetermined, among one or more sub-records in each of the nucleic acid records (Claim 8)
(b-2-2-4) retrieving nucleic acid sequence data corresponding to the determined valid sub-record and identification information thereof (Claim 8),
(ii) sorting the selected nucleic acid sequence data according to whether the selected nucleic acid sequence data are included in a reference sequence (RefSeq) database, wherein the ranking is higher when the nucleic acid sequence data are included in the RefSeq database than when not included (Claim 9)
(i) sorting the selected nucleic acid sequence data according to the assembly level, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order; and (Claim 9)
wherein the method further comprises, between steps (b) and (c), the following steps: (b-3) sorting the retrieved nucleic acid sequence data according to the biosample identification to select nucleic acid sequence data having the same biosample identification; (b-4) sorting the selected nucleic acid sequence data so as to satisfy at least one of the following sort criteria; (b-5) selecting a nucleic acid sequence of the highest-ranked nucleic acid sequence data among the sorted nucleic acid sequence data; and (b-6) deleting nucleic acid sequence data except for the highest-ranked nucleic acid sequence data from the retrieved nucleic acid sequence data, wherein the sort criteria include the following; (Claim 9)
(ii) sorting according to whether the nucleic acid sequence data are included in a reference sequence (RefSeq) database, wherein the ranking is higher when the nucleic acid sequence data are included in the RefSeq database than when not included (Claim 10)
(iv) sorting according to the length of the nucleic acid sequence data, wherein the longer the length, the higher the ranking; (v) sorting according to whether there is description in a host of a descriptor of a nucleic acid record containing the nucleic acid sequence data, wherein the ranking is higher when a host of interest for the organism of interest is described in the host than when not described, and higher when an organism different from the organism of interest are not described in the host than when described; (Claim 10)
(vi) sorting according to the registration date or revision date of a nucleic acid record containing the nucleic acid sequence data, wherein the more recent the registration date or revision date, the higher the ranking; (Claim 10)
(i) sorting according to the assembly level of the nucleic acid sequence data, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order (Claim 10)
(vii) sorting according to the alphabetical order in accession number of the nucleic acid sequence data, wherein the earlier the alphabetical order of the accession number, the higher the ranking (Claim 10) (iii) sorting according to whether a name of a nucleic acid molecule described in a descriptor of a nucleic acid record containing the nucleic acid sequence data is identical to at least one of the received name of the target nucleic acid and the retrieved synonyms, wherein the ranking is higher when identical than when not identical (Claim 10),
(iii) sorting according to whether there is a description in a host of a descriptor of a nucleic acid record containing the selected taxonomic representative sequence, wherein the ranking is higher when a host of interest for the organism of interest is described in the host than when not described, and higher when an organism different from the host of interest is not described in the host than when described (Claim 11)
(iv) sorting according to the alphabetic order of accession number in the selected taxonomic representative sequence, wherein the earlier the alphabetic order of the accession number, the higher the ranking (Claim 11)
(i) sorting according to the assembly level of the selected taxonomic representative sequence, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order (Claim 11)
wherein the selecting of the group representative sequence in step (d) is performed by a method including the following steps: (d-1) sorting the selected taxonomic representative sequences so as to satisfy at least one of the following predetermined sort criteria; (d-2) selecting the highest-ranked taxonomic representative sequence among the sorted taxonomic representative sequences; and (d-3) grouping taxonomic representative sequences having a homology of a predetermined value or more with the highest-ranked taxonomic representative sequence and selecting the highest-ranked taxonomic representative sequence as the group representative sequence in each group, wherein the sort criteria include the following (Claim 11)
(ii) the number of nucleic acid sequence data having the same taxonomic name and/or taxonomic ID as the selected taxonomic representative sequence, wherein the larger the number, the higher the ranking (Claim 11)
wherein the target nucleic acid sequence data set provided in step (f) has a homology of a predetermined value or more with at least one representative sequence of the group representative sequences and the taxonomic representative sequences for the target nucleic acid sequence data set (Claim 13)
wherein the non-target nucleic acid sequence data set provided in step (g) satisfies at least one of the following homology criteria: (i) the non-target nucleic acid sequence data set needs to have a homology of a predetermined value or more with a partial sequence region of at least one representative sequence of the group representative sequence and the taxonomic representative sequence; (ii) the non-target nucleic acid sequence data set needs to have a homology of a predetermined value or more with at least one representative sequence of the group representative sequence and the taxonomic representative sequence; and (iii) the non-target nucleic acid sequence data set having homology criterion (i) needs to have homology criterion (ii) (Claim 15)
(e) retrieving nucleic acid sequence data having a homology of a predetermined value or more with the group representative sequence to provide the retrieved nucleic acid sequence data as a nucleic acid sequence data set for the design of an oligonucleotide (Claim 19))
computer readable storage medium containing instructions to configure a processor to perform a method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising (Claim 19)
(d) grouping the selected taxonomic representative sequences according to homology and selecting a group representative sequence for each group; and (Claim 19)
(c) sorting the retrieved nucleic acid data according to taxonomic name and/or taxonomic identification (ID) and selecting taxonomic representative sequences among nucleic acid sequence data having the same taxonomic name and/or taxonomic ID (Claim 19)
(b) retrieving nucleic acid sequence data included in nucleic acid records, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule and the retrieved synonyms are described (Claim 19)
With respect to the limitations of Claims 1, 3, 10, 11, 19, Sayers teaches the core of Entrez is an engine that performs two basic tasks for any Entrez database: 1) assemble a list of UIDs that match a text query, and 2) retrieve a brief summary record called a Document Summary (DocSum) for each UID. When Queried with the organism name and the gene name. Entrez will assemble a list of UIDs that match. Ebtrez uses a query function of (organism+ term) against a database of records. This inherently includes categories of records for part or the entirety of the target nucleic acid molecule or variant nucleic acid sequence data for the target nucleic acid molecule. Entrez retrieval already turns on whether the query term appears in a record’s descriptor fields, offering records whose descriptor name is identical to the target name. The precise rank is a routine ordering choice. (pg. 6, paragraph 1, (b) retrieving nucleic acid sequence data included in nucleic acid records, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule and the retrieved synonyms are described (Claim 1), wherein the nucleic acid sequence data in step (b) include nucleic acid sequence data corresponding to a part or the entirety of the target nucleic acid molecule or variant nucleic acid sequence data for the target nucleic acid molecule (Claim 3), (iii) sorting according to whether a name of a nucleic acid molecule described in a descriptor of a nucleic acid record containing the nucleic acid sequence data is identical to at least one of the received name of the target nucleic acid and the retrieved synonyms, wherein the ranking is higher when identical than when not identical (Claim 10), (iii) sorting according to whether there is a description in a host of a descriptor of a nucleic acid record containing the selected taxonomic representative sequence, wherein the ranking is higher when a host of interest for the organism of interest is described in the host than when not described, and higher when an organism different from the host of interest is not described in the host than when described (Claim 11) (b) retrieving nucleic acid sequence data included in nucleic acid records, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule and the retrieved synonyms are described (Claim 19)
With respect to the limitations of Claims 4, 8, 10, 11, Sayers teaches EFetch can retrieve any sequence record by its accession.version identifier, including sequences that do not have GI numbers. The EFetch is a search call that yields identifiers, followed by a fetch on these identifiers. Accession.version is the standard identifier used in the database. It is a routine design choice to order the provided information in alphabetical order. (pg. 5, paragraph 1, wherein the retrieving of nucleic acid sequence data in the step (b) is performed by the method comprising the following steps: (b-1) retrieving identifiers of nucleic acid records, wherein each of the nucleic acid records is associated with the organism of interest and comprises a descriptor in which at least one of the name of the target nucleic acid molecule and the retrieved synonyms are described; and (b-2) retrieving nucleic acid sequence data specified by the identifiers (Claim 4), wherein in step (b-2-2), the nucleic acid sequence data corresponding to the target nucleic acid molecule and identification information of the nucleic acid sequence data are selectively retrieved from the nucleic acid records, wherein the selective retrieving of the nucleic acid sequence data and the identification information of the nucleic acid sequence data includes the following steps: (b-2-2-1) determining, as a valid sub-record, a sub-record in which the synonym is recorded in a first specification that is predetermined, among one or more sub-records in each of the nucleic acid records (Claim 8), (b-2-2-4) retrieving nucleic acid sequence data corresponding to the determined valid sub-record and identification information thereof (Claim 8), (vii) sorting according to the alphabetical order in accession number of the nucleic acid sequence data, wherein the earlier the alphabetical order of the accession number, the higher the ranking (Claim 10), (iv) sorting according to the alphabetic order of accession number in the selected taxonomic representative sequence, wherein the earlier the alphabetic order of the accession number, the higher the ranking (Claim 11)
With respect to the limitations of Claim 7, Sayers teaches the display format function is performed by EFetch, which generates formatted output for a list of input UIDs which includes the nucleic acid sequence data (pg. 6, paragraph 7, wherein step (b-2) includes the following steps: (b-2-1) retrieving nucleic acid records specified by the identifiers; and (b-2-2) retrieving nucleic acid sequence data corresponding to the target nucleic acid molecule from the nucleic acid records (Claim 7))
With respect to the limitations of Claims 1, 19, Kitts et al. teaches the next hierarchy provides access to all assemblies for the species, latest assemblies, or selected reference or representative assemblies for the species (if any). This shows the data is organizes sequence/ assembly data for each species grouped per taxon. (pg. D77, col. 2, paragraph 4 – pg. D78, col. 1, paragraph 1, (c) sorting the retrieved nucleic acid data according to taxonomic name and/or taxonomic identification (ID) and selecting taxonomic representative sequences among nucleic acid sequence data having the same taxonomic name and/or taxonomic ID (Claim 1), (c) sorting the retrieved nucleic acid data according to taxonomic name and/or taxonomic identification (ID) and selecting taxonomic representative sequences among nucleic acid sequence data having the same taxonomic name and/or taxonomic ID (Claim 19)
With respect to the limitations of Claims 9, 10, 11, Kitts et al. teaches that even the combination of BioProject ID and BioSample ID is not sufficient to identify assemblies since there are examples of multiple assemblies generated from the same set of sequencing reads using different assembly algorithms. The claim removes duplicate genome records that only differ because the same biological sample was deposited more than once (pg. D74, col. 1, paragraph 1, wherein the method further comprises, between steps (b) and (c), the following steps: (b-3) sorting the retrieved nucleic acid sequence data according to the biosample identification to select nucleic acid sequence data having the same biosample identification; (b-4) sorting the selected nucleic acid sequence data so as to satisfy at least one of the following sort criteria; (b-5) selecting a nucleic acid sequence of the highest-ranked nucleic acid sequence data among the sorted nucleic acid sequence data; and (b-6) deleting nucleic acid sequence data except for the highest-ranked nucleic acid sequence data from the retrieved nucleic acid sequence data, wherein the sort criteria include the following; (Claim 9) Kitts et al. also teaches the model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The NCBI records each assembly along a contig to scaffold to chromosome to complete genome. The specific order chosen is routine optimization that can be done by any persona having ordinary skill in the art. (abstract, (i) sorting the selected nucleic acid sequence data according to the assembly level, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order; and (Claim 9), wherein the selecting of the taxonomic representative sequence in step (c) is performed by a method including the following steps: (c-1) sorting the nucleic acid sequence data having the same taxonomic name and/or taxonomic ID so as to satisfy at least one of the following predetermined sort criteria; and (c-2) selecting, as the taxonomic representative sequence, a nucleic acid sequence of the highest-ranked nucleic acid sequence data among the sorted nucleic acid sequence data, wherein the predetermined sort criteria include the following: (i) sorting according to the assembly level of the nucleic acid sequence data, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order (Claim 10), : (i) sorting according to the assembly level of the selected taxonomic representative sequence, wherein as for the assembly level, complete genome, chromosome, scaffold, and config are ranked higher in that order (Claim 11) Kitts et al. also teaches to track assembly updates so that users can see the history of previous versions for an assembly. Preferring the most recent registration for sorting is a design choice (pg. D73, col. 2, paragraph 3, (vi) sorting according to the registration date or revision date of a nucleic acid record containing the nucleic acid sequence data, wherein the more recent the registration date or revision date, the higher the ranking; (Claim 10)
With respect to the limitations of Claims 1, 10, 11, 19, Li et al. teaches sequences are first sorted in order of decreasing length. The longest sequence becomes the representative of the first cluster. Then, each remaining sequence is compared with the representatives of existing clusters. If the similarity with any representative is above a given threshold, It is grouped into that cluster. Otherwise, a new cluster is defined with that sequence as the representative. CD-Hit groups each sequence into that cluster when its similarity of any representative is above a certain threshold. The host field is standard in GenBank. Preferring records whose host field matches the organism of interest is ranking by one available metadata field. Counting how many records share a taxon is a direct by product of the grouping and preferring the most well represented taxon is routine optimization any person having ordinary skill in the art would accomplish. (pg. 1659, col. 1, paragraph 2, (d) grouping the selected taxonomic representative sequences according to homology and selecting a group representative sequence for each group; and (Claim 1), (iv) sorting according to the length of the nucleic acid sequence data, wherein the longer the length, the higher the ranking; (v) sorting according to whether there is description in a host of a descriptor of a nucleic acid record containing the nucleic acid sequence data, wherein the ranking is higher when a host of interest for the organism of interest is described in the host than when not described, and higher when an organism different from the organism of interest are not described in the host than when described; (Claim 10), wherein the selecting of the group representative sequence in step (d) is performed by a method including the following steps: (d-1) sorting the selected taxonomic representative sequences so as to satisfy at least one of the following predetermined sort criteria; (d-2) selecting the highest-ranked taxonomic representative sequence among the sorted taxonomic representative sequences; and (d-3) grouping taxonomic representative sequences having a homology of a predetermined value or more with the highest-ranked taxonomic representative sequence and selecting the highest-ranked taxonomic representative sequence as the group representative sequence in each group, wherein the sort criteria include the following (Claim 11), (ii) the number of nucleic acid sequence data having the same taxonomic name and/or taxonomic ID as the selected taxonomic representative sequence, wherein the larger the number, the higher the ranking (Claim 11), (d) grouping the selected taxonomic representative sequences according to homology and selecting a group representative sequence for each group; and (Claim 19),
With respect to the limitations of Claims 1, 13, 15, 19, Camacho et al teaches Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program that can be used to quickly search a sequence database for matches to a query sequence. A Blast search will return all sequences in the database above a chosen similarity metric of the searched sequence while giving a predetermined value to each sequence. (pg. 1, col. 1, paragraph 1, (e) retrieving nucleic acid sequence data having a homology of a predetermined value or more with the group representative sequence to provide the retrieved nucleic acid sequence data as a nucleic acid sequence data set for the design of an oligonucleotide (Claim 1), wherein the target nucleic acid sequence data set provided in step (f) has a homology of a predetermined value or more with at least one representative sequence of the group representative sequences and the taxonomic representative sequences for the target nucleic acid sequence data set (Claim 13), wherein the non-target nucleic acid sequence data set provided in step (g) satisfies at least one of the following homology criteria: (i) the non-target nucleic acid sequence data set needs to have a homology of a predetermined value or more with a partial sequence region of at least one representative sequence of the group representative sequence and the taxonomic representative sequence; (ii) the non-target nucleic acid sequence data set needs to have a homology of a predetermined value or more with at least one representative sequence of the group representative sequence and the taxonomic representative sequence; and (iii) the non-target nucleic acid sequence data set having homology criterion (i) needs to have homology criterion (ii) (Claim 15), (e) retrieving nucleic acid sequence data having a homology of a predetermined value or more with the group representative sequence to provide the retrieved nucleic acid sequence data as a nucleic acid sequence data set for the design of an oligonucleotide (Claim 19))
With respect to the limitations of Claim 6, Camacho et al teaches for long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. Selectively extracting the target gene’s region from a multi-gene record uses the standard feature annotation in every GeneBank record; that records carry such coordinates and that tools retrieve only the relevant part is established. The specific automated parsing logic is just routine application of those standard annotations (abstract, nucleic acid sequence data corresponding to the target nucleic acid molecule are selectively retrieved in the nucleic acid sequence data specified by the identifiers (Claim 6))
With respect to the limitations of Claims 1, 9, 10, 19, O’Leary et al teaches a computer program that has the RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. This treats a record as higher ranked if it is included in the RefSeq database. (abstract, A computer-implemented method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising (Claim 1), (ii) sorting the selected nucleic acid sequence data according to whether the selected nucleic acid sequence data are included in a reference sequence (RefSeq) database, wherein the ranking is higher when the nucleic acid sequence data are included in the RefSeq database than when not included (Claim 9), (ii) sorting according to whether the nucleic acid sequence data are included in a reference sequence (RefSeq) database, wherein the ranking is higher when the nucleic acid sequence data are included in the RefSeq database than when not included (Claim 10), computer readable storage medium containing instructions to configure a processor to perform a method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest, the method comprising (Claim 19)
A person of ordinary skill in the art would be motivated to combine Malgott et al. in view of Sayers in further view of Kitts et al. in further view of Li et al. in further view of Camacho et al. in further view of O’Leary et al. as each work is in a common field of retrieval and curation of nucleic acid sequence records from a public database. The works directly address the problem the applicant is trying to solve of conventional sequence retrieval and curation for oligonucleotide design is incomplete and researcher dependent. Therefore there is a strong motivation for a person having ordinary skill in the art to combine Malgott et al. in view of Sayers in further view of Kitts et al. in further view of Li et al. in further view of Camacho et al. in further view of O’Leary et al. in order to address the problem. There is a reasonable expectation of success because each component was already an independent working system. The instant application just combines previously known steps without changing how they work individually so they are expected to continue to work when combined.
Claims 12, 14 are rejected under 35 U.S.C. 103 as being unpatentable Malgott et al. in view of Sayers in further view of Kitts et al. in further view of Li et al. in further view of Camacho et al. in further view of O’Leary et al. as applied to claims 1-11, 13, 15, 19 above in further view of Ye et al. (Ye, J.; Coulouris, G.; Zaretskaya, I.; Cutcutache, I.; Rozen, S.; Madden, T. L. Primer-BLAST: A Tool to Design Target-Specific Primers for Polymerase Chain Reaction. BMC Bioinformatics 2012, 13 (1).) The italicized text corresponds to the instant claim limitations.
The limitations of claims 1-11, 13, 15, 19 have been taught by Malgott et al. in view of Sayers in further view of Kitts et al. in further view of Li et al. in further view of Camacho et al. in further view of O’Leary et al. above.
Malgott et al. in view of Sayers in further view of Kitts et al. in further view of Li et al. in further view of Camacho et al. in further view of O’Leary et al. does not explicitly teach
wherein the method further comprises step (f) of providing, as a target nucleic acid sequence data set for the target nucleic acid molecule, nucleic acid sequence data associated with the received organism of interest in the nucleic acid sequence data set provided in step (e) (Claim 12)
wherein the method further comprises step (g) of providing, as a non-target nucleic acid sequence data set for a non-target nucleic acid molecule, nucleic acid sequence data not associated with the received organism of interest from the nucleic acid sequence data set provided in step (e) (Claim 14)
However, these limitations were known in the art at the time of the effective filing date of the invention, as taught by Ye et al.
With respect to the limitations of Claim 12, Ye et al. teaches that specific amplification of the intended target requires that primers do not have matches to other targets in certain orientations and within certain distances that allow undesired amplification. Oligonucleotide design distinguishes the intended target organism sequence from everything else. Primer-Blast is built on that intended target algorithm (abstract, wherein the method further comprises step (f) of providing, as a target nucleic acid sequence data set for the target nucleic acid molecule, nucleic acid sequence data associated with the received organism of interest in the nucleic acid sequence data set provided in step (e) (Claim 12)
With respect to the limitations of Claim 14, Ye et al. teaches the specificity checking module by default uses BLAST search parameters that ensure high sensitivity such that it can detect a target that contains up to 35% mismatches to the primer sequence (pg. 3, col. 1, paragraph 3, wherein the method further comprises step (g) of providing, as a non-target nucleic acid sequence data set for a non-target nucleic acid molecule, nucleic acid sequence data not associated with the received organism of interest from the nucleic acid sequence data set provided in step (e) (Claim 14))
A person having ordinary skill in the art would be motivated to combine the method for providing a nucleic acid sequence data set for the design of an oligonucleotide used to detect a target nucleic acid molecule of an organism of interest as taught by Malgott et al. in view of Sayers in further view of Kitts et al. in further view of Li et al. in further view of Camacho et al. in further view of O’Leary et al. with Ye et al. as each work is in a common field of retrieval and curation of nucleic acid sequence records from a public database. There is a reasonable expectation of success because each component was already an independent working system. The instant application just combines previously known steps without changing how they work individually so they are expected to continue to work when combined.
Conclusion
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/C.H.B./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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