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 11/23/2021 is a Continuation of PCT/ US20 /34329, filed 05/22/2020 , and claims priority from Provisional Application 62852794, filed 05/24/2019 , and Provisional Application 62878238, filed 07/24/2019 . T he claims are therefore examined as filed on 05/24/2019 , 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 15 and 31-49 are pending. Claims 39 and 49 are objected to. Claims 1-14 and 16-30 are cancelled. Claims 15 and 31-49 are examined. Claims 15 and 31-49 are rejected. Information Disclosure Statement The Information Disclosure Statements are in compliance with the provisions of 37 CFR 1.97. Accordingly, all references have been considered. Claim Objections Claim s 39 and 49 are objected to because of the following informalities: In claim 39, the phrase “configured to displaying” should be corrected to “configured to displaying display ” In claim 49, the phrase “A non-transitory computer-readable storage media” should be corrected to “A non-transitory computer-readable storage media medium ” Appropriate correction is required. 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 15 and 31-49 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 15 and 31-37 are directed to a process (computer implemented method), claims 38-48 are directed to a machine product (a system comprising a computing device with a processor, operating system, and memory ), and claim 49 is also directed to a product (a non-transitory computer readable medium). 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: Determining a genetic similarity between nucleic acid sequence information from two pathogen strains (mental process; the human mind is capable of comparing data for similarities/comparing two data strings; claims 15, 38, 49) Identifying a pathogen strain as the same as a second pathogen strain based on genetic similarity (mental process; the human mind is capable of matching data to determine if two things are the same based on similarity; claims 15, 38, 49) Estimating a future sample location for a pathogen strain with a non-linear classification algorithm based on source locations calculated at different sampling times (mental process/mathematical concept; the human mind is capable of applying a mathematical classification algorithm to data, and doing so is equivalent to performing a calculation, the specification [00741] indicates this classification is done using one of many possible statistical classification techniques; claims 15, 38, 49) Determining a source location by identifying the source location of a contamination based on sampling time and genetic distance between pathogen strains (mental process ; the human mind is capable of making a determination based on analysis of data; claims 16, 44) Determining genetic distances between a nucleic acid derived from a pathogen strain and a second pathogen strain (mental process/mathematical concept; the human mind is capable of computing a genetic distance between nucleic acids from two nucleic acid sequences, which is done using a calculation; claim 36 specifies this is done in part by calculating a number of unique nucleic acid pairs between two orthologous or paralogous genes belonging to both pathogens , claims 34-36, 48) Ranking samples contaminated with a pathogen according to sampling time to identify the source of contamination (mental process/mathematical concept; the human mind is capable of ranking data according to time, ranking using numerical values is a mathematical concept; claim 37 ) 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. The claims do not recite additional elements to the abstract ideas listed in step (1) and therefore cannot integrate the judicial exception into a practical application. Claim 15 and its dependents recite the additional element s of the method being computer-implemented, claim 38 and its dependents recite the additional element of a system comprising a computing device comprising a processor, an operating system a memory and a computer program with executable instructions, and claim 49 recites the additional element of a non-transitory computer readable medium. The claims also recite t he additional elements of receiving nucleic sequence information and metadata from the computer /system , and using the computer /system to output data after analysis. Claims 32 specifies that the nucleic acid sequencing information is obtained from samples. Claim 3 3 also recites the additional element of sequencing the pathogens to obtain nucleic sequence information. Claims 40-43 also recite the additional element of displaying data on a graphical map through an output software module, and claims 45-47 recite the additional element of a sequencer for sequencing the pathogen strain, with claim 46 specifying that the sequencer is a nanopore sequencer. While the claims recite the additional element of receiving and outputting data, such step s that only amount to necessary data gathering and outputting , without any technical details of how the data is obtained / output that integrate the judicial exception, are insignificant extrasolution activit ies that do not add a meaningful limitation to the claims (see MPEP 2106.05(g)). Similarly, the use of a sequencer for gathering/generating data and a display for outputting data merely indicates a field of use or technological environment in which to apply a judicial exception (see MPEP 2106.05(h)). As a result, the judicial exception is not integrated into a practical application. In addition , w hile the claims recite additional elements related to the use of computers , they do not provide any specific details by which the computer, processor, memory, or software on a readable medium 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 produce data do not provide an inventive concept. Non-particular instructions to receive or output data using general computer elements 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) . Further, the use of a sequencer, and specifically a nanopore to sequence nucleic acids, is also considered a well-understood, routine and conventional activit y as evidenced by the specification [00431] which describes several commercially available sequencers, including a nanopore sequencing system . 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. 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. Claim Rejection Claim s 15, 32-33, 37- 38 , 45, 47, and 49 are rejected under 35 U.S.C. 103 as being unpatentable over THOMAS 2017 “Food Pathogen Bioinformatics” ( US 20170124253 A1 ) in view of BELANCHE -MUNOZ 2008 “ Machine learning methods for microbial source tracking .” Claim Interpretation and Scope and Contents of Prior Art Claims 15, 38, and 49 recite a computer-implemented method, system and a computer-readable medium containing a program for monitoring a pathogen strain, for performing the steps of (a) receiving, at the computer, first nucleic acid sequence information from said pathogen strain obtained from a first location at a first time; (b) receiving, at the computer, second nucleic acid sequence information from a second pathogen strain obtained from a second location at a second time; and (c) receiving, at the computer, metadata comprising the first location and time, and second location and time. With respect to this limitation, THOMAS teaches systems and methods for identifying the spread of pathogens in food over space and time, including the use of a computer for receiving genomic data and metadata with time and location that for a first pathogen source and a second pathogen source [0008-11, claims 13-14]. Claims 15, 38, and 49 also recite the limitations of steps (d) determining a genetic similarity between the first nucleic acid sequence information from the pathogen strain and the second nucleic acid sequence information from the second pathogen strain; and (e) identifying the pathogen strain as the same as the second pathogen strain based, at least in part, on the genetic similarity . With respect to this limitation, THOMAS also teaches comparing the first genomic sequence data of the first pathogen to second genomic sequence data derived from a second food pathogen and determining whether the first food pathogen and the second food pathogen are of a same strain based on the comparison [0010, 0104-110, claim 13] . Claims 15, 38, and 49 also recite the limitations of step (f) determining a source location of a contamination from said pathogen strain based at least in part, on the metadata (g) repeating (a) to (f) to output a plurality of source locations at different sampling times . With respect to this limitation, THOMAS also teaches locating the source of contamination in space and time [0049] based on the metadata, which includes time and location [0035], and also teaches automatically repeating the process with newly received genetic information to determine other samples/sources [0049-50] . Claims 15, 38, and 49 also recite the limitations of step (h) of estimat ing a future sample location for the pathogen strain with a non-linear classification algorithm based on the plurality of source locations calculated at said different sampling times . THOMAS does not teach th is limitation ; however BELANCHE -MUNOZ teaches determining future sample locations for a microbe using various classification algorithm methods, including nonlinear methods such as k-nearest-neighbor and quadratic Bayesian (Abstract), and it would be obvious to one of ordinary skill in the art to apply one of these methods using the data and methods of THOMAS to predict future sample locations. Claim 32 recites the limitation wherein the first nucleic acid sequence information and second nucleic acid sequence information are obtained from one or more samples from a plurality of physical locations at a plurality of different times. With respect to this limitation, THOMAS teaches that genomic data/metadata can be obtained from a sample from different locations and different times as it is transported [0086-87] . Claim 33 recites the limitation of sequencing the pathogen strain or the second pathogen strain to obtain the first and second nucleic acid sequence information, claim 45 recites using a nucleic acid sequencer to sequence the pathogen strains, and claim 47 recites the limitation of receiving the nucleic acid sequence information from the nucleic acid sequencer. With respect to these limitations, THOMAS teaches sequencing the pathogens and receiving the genetic information from a sequencer [0008, 16, 0049] . Claim 37 recites the limitation of ranking samples contaminated with the pathogen strain according to a sampling time to identify an earliest contaminated sample representing the source of the contamination. With respect to this limitation, THOMAS teaches determining the source of contamination by recognizing relations among contamination events in space and time [0049], and one of ordinary skill in the art would understand that contaminations ranked earlier in time are closer to a source. Resolving Ordinary Skill in the Art and Obviousness Rationale A teaching, suggestion, or motivation in the prior art would have led one of ordinary skill in the art to modify or combine the prior art to arrive at the claimed invention. Specifically, a person of ordinary skill in pathogen source tracking would have been motivated to combine the teachings of THOMAS with the teachings of BELANCHE -MUNOZ , in order to achieve the claimed invention , because many statistical models are useful for accurately predicting and tracking pathogen spread (Abstract), and a nonlinear model (quadradic Bayesian classifier) in particular gave a higher percentage of correct classification for the training set of observations compared to a linear model (linear Bayesian classifier; pg 745 last par and 746 first par) . A person of ordinary skill would reasonably expect success from combining these teachings, as both THOMAS and BELANCHE -MUNOZ teach methods of tracking pathogen spread, and because any of the algorithms of BELANCHE -MUNOZ can be applied using the data of THOMAS to predict pathogen spread . Therefore, the claims at issue would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention as there is both a reason to modify or combine the prior art, and a reasonable expectation of success (see MPEP 2143.02 (I)). Claim Rejection Claims 31, 34 -36 , 44, and 48 are rejected under 35 U.S.C. 103 as being unpatentable over THOMAS in view of BELANCHE -MUNOZ as applied to claims 15, 32-33, 37-38, 45, 47, and 49 above, and further in view of PETTENGILL 2016 “Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k- mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.” Claim Interpretation and Scope and Contents of Prior Art THOMAS in view of BELANCHE -MUNOZ teaches the limitations of claims 15, 32-33, 37-38, 45, 47, and 49 above. Claims 31 and 44 recite the limitation of identifying source location from the contamination based on sampling time and a genetic distance between said pathogen strain and said second pathogen strain. With respect to this limitation, THOMAS teaches using analyses such as using a matrix and phylogenic tree (which would show the genetic divergence, the genetic distance) along with location metadata to determine the source [0011,14, claim 5], but does not specifically teach calculating genetic distance to identify the source. However, PETTENGILL teaches methods of determining genetic distance in pathogen samples for tracking outbreaks (Abstract) than can be applied to the data of THOMAS to help determine a source. Claims 34 and 48 recite the limitations of determining a plurality of genetic distances between a nucleic acid derived from the first pathogen strain and second pathogen strain. With respect to these limitations, THOMAS teaches using analyses such as using a matrix and phylogenic tree (which would show the genetic divergence, the genetic distance), but does not specifically teach determining a plurality of genetic distances. However, PETTENGILL teaches methods of determining genetic distance in pathogen samples for tracking outbreaks (Abstract) that one of ordinary skill would be motivated to apply to the data of THOMAS to identify a pathogen. Claim 3 5 recites the limitation wherein the plurality of genetic distances are computed between at least two orthologous or paralogous genes belonging to the pathogen strain and said second pathogen strain. THOMAS also does not teach this limitation, however PETTENGILL teaches methods of determining genetic distance between ortholog genes ( pg 3 par 3) . Claim 36 recites the limitation wherein a genetic distance of said plurality of genetic distances is determined at least in part by calculating a number of unique nucleic acid base pairs between the orthologous or paralogous genes belonging to the pathogen strain and second pathogen strain. THOMAS also does not teach this limitation, however PETTENGILL teaches methods of determining genetic distance between ortholog genes and counting the number of base pair mismatches ( pg 3 par 3). Resolving Ordinary Skill in the Art and Obviousness Rationale A teaching, suggestion, or motivation in the prior art would have led one of ordinary skill in the art to modify or combine the prior art to arrive at the claimed invention. Specifically, a person of ordinary skill in pathogen source tracking would have been motivated to combine the teachings of THOMAS in view of BELANCHE -MUNOZ with the teachings of PETTENGILL , in order to achieve the claimed invention, because computing genetic distance allows for identification plausibly relevant samples as part of outbreak tracking ( pg 2 par 2) . A person of ordinary skill would reasonably expect success from combining these teachings, as both THOMAS in view of BELANCHE -MUNOZ and PETTENGILL teach methods of tracking pathogen spread, and because the methods of computing genetic distance in PETTENGILL can be applied using the data of THOMAS to access sample relatedness . Therefore, the claims at issue would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention as there is both a reason to modify or combine the prior art, and a reasonable expectation of success (see MPEP 2143.02 (I)). Claim Rejection Claims 39-43 are rejected under 35 U.S.C. 103 as being unpatentable over THOMAS in view of BELANCHE -MUNOZ as applied to claims 15, 32-33, 37-38, 45, 47, and 49 above, and further in view of HOFFMANN 2016 “Tracing Origins of the Salmonella Bareilly Strain Causing a Food-borne Outbreak in the United States.” Claim Interpretation and Scope and Contents of Prior Art THOMAS in view of BELANCHE -MUNOZ teaches the limitations of claims 15, 32-33, 37-38, 45, 47, and 49 above. Claim 39 recites the limitation of the system using an output software module configured to display source location of contamination from the pathogen strain on a graphical map . With respect to this limitation, THOMAS teaches sharing source locations by network connections [0009, 56] but does not specifically teach displaying the source location on a graphical map. However, HOFFMANN teaches methods for geographically mapping transmission of a pathogen to source track its outbreak (Abstract, pg 503 par 1) which can be applied in the methods and system of THOMAS to display the source location of contamination . Claim 40 recites the limitation wherein the output software module is further configured to display the first location and second location on said graphical map. With respect to this limitation, HOFFMANN teaches geographically mapping transmission of a pathogen across different locations (Abstract, pg 503 par 1, Fig 2). Claim 41 recites the limitation wherein the output software module is further configured to display the first time and second time along with said first location and said second location on said graphical map. With respect to this limitation, HOFFMANN teaches that the geographical map can display locations of contamination events ( pg 507 par 1), and it would be obvious to one of ordinary skill in the art to include the time data for the events from THOMAS to identify sources. Claim 42 recites the limitation wherein the output software module is further configured to display one or more parameters not associated with sampling on the graphical map. With respect to this limitation, HOFFMANN teaches that the geographical map can display different parameters, such as betweenness and historical frequency of transmission, through node size and color and arrow line thickness (Fig 2). Claim 43 recites the limitation wherein the one or more parameters not associated with sampling comprises:(a) employee movement patterns or residency at one or more of the locations on the graphical map; (b) production quantities of a product at one or more locations on the graphical map; (c) product flow between one or more locations on the graphical map; or (d) reagent input flow between one or more locations on said graphical map; or (e) any combination of (a) to (d). With respect to this limitation, THOMAS teaches that metadata can include personnel that came into contact with the sample at various times and the location of the sample while in transit, while HOFFMANN teaches that the geographical map can display different parameters, such as betweenness and historical frequency of transmission, through node size and color and arrow line thickness (Fig 2); it would be obvious to one of ordinary skill in the art to substitute parameters from THOMAS into the map of HOFFMANN to visualize the spread of the pathogen. Resolving Ordinary Skill in the Art and Obviousness Rationale A teaching, suggestion, or motivation in the prior art would have led one of ordinary skill in the art to modify or combine the prior art to arrive at the claimed invention. Specifically, a person of ordinary skill in pathogen source tracking would have been motivated to combine the teachings of THOMAS in view of BELANCHE -MUNOZ with the teachings of HOFFMANN , in order to achieve the claimed invention, because combining genomic analysis with geographical mapping tools allows for creation of graphs for visualizing pathogen spread that allows for better understanding of a transmission network ( pg 503 par 1) . A person of ordinary skill would reasonably expect success from combining these teachings, as both THOMAS in view of BELANCHE -MUNOZ and HOFFMANN teach methods of tracking pathogen spread, and because the methods of geographic mapping in HOFFMANN can be applied using the data of THOMAS to visualize the pathogen spread . Therefore, the claims at issue would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention as there is both a reason to modify or combine the prior art, and a reasonable expectation of success (see MPEP 2143.02 (I)). Claim Rejection Claim 4 6 is rejected under 35 U.S.C. 103 as being unpatentable over THOMAS in view of BELANCHE -MUNOZ as applied to claims 15, 32-33, 37-38, 45, 47, and 49 above, and further in view of SEKSE 2017 “High Throughput Sequencing for Detection of Foodborne Pathogens.” Claim Interpretation and Scope and Contents of Prior Art THOMAS in view of BELANCHE -MUNOZ teaches the limitations of claims 15, 32-33, 37-38, 45, 47, and 49 above. Claim 46 recites the limitation wherein said nucleic acid sequencer comprises a nanopore sequencer. With respect to this limitation, THOMAS teaches using high-throughput whole genome sequencing technology to identify food pathogens on the strain level [0049], but does not specify that the sequencer comprises a nanopore sequencer. However, SEKSE reviews current methods of high throughput sequencing for detection of foodborne pathogens, which includes nanopore sequencing using the Oxford Nanopore MinION (Abstract, pg 3 col 2). Resolving Ordinary Skill in the Art and Obviousness Rationale A teaching, suggestion, or motivation in the prior art would have led one of ordinary skill in the art to modify or combine the prior art to arrive at the claimed invention. Specifically, a person of ordinary skill in pathogen detection would have been motivated to combine the teachings of THOMAS in view of BELANCHE -MUNOZ with the teachings of SEKSE , in order to achieve the claimed invention, because high throughput sequencing methods, including the use of a nanopore sequencer, are conventional and well-known methods of sequencing applied in foodborne pathogen analysis that can provide longer reads in real-time at low costs (Abstract, pg 3 col 2) . A person of ordinary skill would reasonably expect success from combining these teachings, as both THOMAS in view of BELANCHE -MUNOZ and SEKSE teach methods of pathogen analysis , and because a nanopore machine can be used to provide the sequencing data used in THOMAS . Therefore, the claims at issue would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention as there is both a reason to modify or combine the prior art, and a reasonable expectation of success (see MPEP 2143.02 (I)). Conclusion Any inquiry concerning this communication or earlier communications from the examiner should be directed to FILLIN "Examiner name" \* MERGEFORMAT MARY C LEVERETT whose telephone number is FILLIN "Phone number" \* MERGEFORMAT (571)272-5494 . The examiner can normally be reached FILLIN "Work Schedule?" \* MERGEFORMAT 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, FILLIN "SPE Name?" \* MERGEFORMAT Karlheinz R. Skowronek can be reached at FILLIN "SPE Phone?" \* MERGEFORMAT (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. / M.C.L ./ Examiner, Art Unit 1687 /Karlheinz R. Skowronek/ Supervisory Patent Examiner, Art Unit 1687