DETAILED ACTION
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 .
Priority
This application filed 09/20/2023 claims foreign priority to 202221058653, filed 10/13/2022. The claims are therefore examined as filed on 10/13/2022, the effective filing date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further review of the priority application(s).
Claim Status
Claims 1-15 are pending.
Claims 1-15 are examined.
Claims 1-15 are rejected.
Information Disclosure Statement
No copy of the publication has been provided for the third listed reference on the IDS filed 09/20/2023, titled “Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps” by DILTHEY et al. Therefore this reference has not been considered. All other references on the IDS are in compliance and have been considered.
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 1-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes and mathematical concepts, without significantly more.
The MPEP at MPEP 2106 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of matter?
(2A)(1) Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea?
(2A)(2) Do the claims recite additional elements that integrate the judicial exception into a practical application?
(2B) If the claims recite a judicial exception and do not integrate the judicial exception, do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?
With regard to step (1) (Are the claims directed to a process, machine, manufacture or composition of matter?): Yes. The claims are directed to one of the statutory classes. Claims 1-5 are directed to a process (processor implemented method), claims 6-10 are directed to a machine product (a system comprising a memory, communication interfaces, and processors), and claims 11-15 are also directed to a product (one or more non-transitory machine-readable information storage mediums).
With regard to step (2A)(1) (Do the claims recite a judicially recognized exception?): Yes. The claims recite the abstract ideas of processing data using mental steps and mathematical concepts. Claims that recite nothing more than abstract ideas, natural phenomena, or laws of nature are not eligible for patent protection (see MPEP 2106.04).
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include but are not limited to:
indexing the plurality of reference genome sequences based on an indexing technique to obtain a reference genome index (mental process; the human mind is capable of organizing data using an index; claims 1, 6, 11)
mapping each of genomic read sequence from the plurality of genomic read sequences to the reference genome index based on a read mapping technique to obtain a read mapping (mental process; the human mind is capable of aligning genomic read sequences to reference sequences; claims 1, 6, 11)
computing a first relative abundance for the plurality of reference genome sequences based on an abundance computation technique using the read mapping (mental process/mathematical concept; the human mind is capable of computing a relative abundance using a computation technique, and doing so is equivalent to performing a calculation; claims 1, 6, 11)
computing a first coverage for each of the reference genomic sequences using a coverage computing technique using the first relative abundance and the read mapping (mental process/mathematical concept; the human mind is capable of computing coverage using a computation technique and data, and doing so is equivalent to performing a calculation; claims 1, 6, 11)
selecting a sub-set of candidate genome sequences from the set of candidate genome sequences to obtain a refined read mapping outcome based on a comparison of the first coverage and the initial pruning threshold (mental process; the human mind is capable of making a selection and comparing a value to a threshold; claims 1, 6, 11)
computing a second relative abundance for the sub-set of candidate genome sequences based on the abundance computation technique using the refined read mapping outcome (mental process/mathematical concept; the human mind is capable of computing a relative abundance using a computation technique and data, and doing so is equivalent to performing a calculation; claims 1, 6, 11)
computing a final relative abundance based on a refinement technique using the termination threshold and an iterative refinement threshold, wherein the refinement technique comprises computing a second coverage for each of the sub-set of candidate genome sequences, based on the coverage computing technique using the second relative abundance (mental process/mathematical concept; the human mind is capable of computing a relative abundance using a computation technique and data, and doing so is equivalent to performing a calculation; claims 1, 6, 11)
estimating the final relative abundance for the sub-set of candidate genome sequences based on the abundance computation technique and the refined read mapping outcome if the termination threshold condition is satisfied, and estimating the final relative abundance for the sub- set of candidate genome sequences based on an iterative refinement technique if the termination threshold condition is not satisfied (mental process/mathematical concept; the human mind is capable of making an estimation based on computed data or using a computation technique, and doing so is equivalent to performing a calculation; claims 1, 6, 11)
Dependent claims 2-5, 7-10, and 12-15 further limit the abstract ideas recited in the independent claims, and do not change their characterization as abstract ideas.
Therefore, the claims recite elements that constitute one or more judicial exceptions.
With regard to step (2A)(2) (Do the claims recite additional elements that integrate the judicial exception into a practical application?): No. Claims 1-5 recite the additional element of a processor for performing the method steps, claims 6-10 recite the additional elements of a system comprising a memory, one or more communication interfaces, and hardware processor coupled to memory via the interfaces, and claims 11-15 recite the additional element of one or more non-transitory machine-readable information storage mediums with instructions to be executed by processors. The claims also recite the additional elements of receiving a plurality of inputs that comprise sequences and thresholds.
While the claims recite the additional element of receiving input data, such steps that only amount to necessary data gathering, without any technical details of how the data is obtained that integrate the judicial exception, are insignificant extrasolution activities that do not add a meaningful limitation to the claims (see MPEP 2106.05(g)). As a result, the judicial exception is not integrated into a practical application. In addition, while the claims also recite additional elements related to the use of computers, they do not provide any specific details by which the system, memory/machine readable medium, communication interfaces, or hardware processor performs or carries out the judicial exception listed in step (2A)(1), nor do they provide any details of how specific structures of the computer are used to implement these functions. The judicial exception is therefore not integrated into a practical application because the generically recited computer elements do not add a meaningful limitation to the abstract idea, as they amount to simply implementing the abstract idea on a computer (see MPEP 2106.05(f)). Because the claims do not recite any additional elements that integrate the judicial exception into a practical application, the claims as a whole are directed to an abstract idea.
With regard to step (2B) (Do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?): No. The claims recite an abstract idea with additional elements; however, these additional elements are general computer elements added to abstract ideas, and non-particular instructions to apply the abstract idea by linking it to a field of use or extrasolution activity (see MPEP 2106.05(f-h)). General computer elements used to perform an abstract idea do not provide an inventive concept, and similarly, non-particular instructions to gather or input data do not provide an inventive concept. Non-particular instructions to gather or input data are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Receiving or transmitting data over a network” from Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362, and “Storing and retrieving information in memory” from Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93 are recognized as conventional activities). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As a result, the claims as a whole do not provide an inventive concept.
Claims Without an Art Rejection
No art rejection is applied to claims 1-15. Close art, for example NALBANTOGLU 2011, while teaching computational analysis of metagenomes using iterative refinement of relative abundance, does not teach at least the claimed limitations of computing a final relative abundance based on a refinement technique using a termination threshold, which comprises a coverage threshold and a cardinality threshold, and an iterative refinement threshold, where the final abundance is estimated based on the abundance computation technique and refined read mapping outcome if the termination threshold condition is satisfied, and estimated based on an iterative refinement technique if it is not. No combinable art before the effective filing date could be found to render the claims as obvious.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
NALBANTOGLU 2011 “RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles” teaches using iterative refinement of relative abundance for metagenomics analysis
PETERSEN 2017 “MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads” teaches a software package to process raw next generation sequence data and perform reference based sequence assignment, and post-processing analysis that includes coverage and relative abundance
AI 2018 “CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads” teaches a pipeline for estimating relative abundance of microbes in a community from metagenomic sequencing data
LINDNER 2013 “Metagenomic abundance estimation and diagnostic testing on species level” teaches a method to estimate true genome abundances via read alignment by considering reference genome similarities in a non-negative LASSO approach
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY C LEVERETT whose telephone number is (571)272-5494. The examiner can normally be reached 8:00am - 5:00pm M-Th.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R. Skowronek can be reached at (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/MARY C LEVERETT/ Examiner, Art Unit 1687
Prosecution Insights