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 .
Applicants Amendment
Applicants amendment filed 7/22/2025 has been received and entered. The specification has been amended. Claims 1, 3, 6, 7-10, 13, 16, 18-20 have been amended, claims 4, 11, 17 have been cancelled.
Claims 1-3, 5-10, 12-16, 18-20, are currently pending.
Election/Restriction
Applicant's election with traverse of group I in the reply filed on 1/9/2025 was acknowledged and upon review it did not appear to be a significant burden to examine the inventions of each of the restricted groups of inventions together. Accordingly, the restriction requirement was withdrawn.
Claims 1-3, 5-10, 12-16, 18-20, drawn to a computer implemented method, a computer product with program instructions, and a computer system.
Priority
This application filed 6/24/2021 makes no claim for priority.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
Response to Applicants Arguments
Applicants summarize the basis of the rejection, and request that the rejection be held in abeyance.
In response, the rejection can not be held in abeyance. In review of the claim amendments, it appears that the present claims are consistent with the claims set forth in ‘498. More specifically, the present claims are broader than ‘498 which focus on the use and analysis of organisms and organization into taxonomic groups, where the instant claims would have to be practiced to provide the necessary k-mers to practice the method of ‘498.
Claims 1-3, 5-10, 12-16, 18-20 stand rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No. 11809498 (application 16/676607). Although the claims at issue are not identical, they are not patentably distinct from each other because both inventions are directed to steps which provide k-mer coverage over genomic sequences where k-mers are divided on the basis of being common and ones being different and being informative to distinguish and/or detect taxonomic differences based on the sequence data of any biological member. Specifically, the steps of ‘498 which require analysis by comparison of kmers that are common and unique and using the unique k-mers for the determination of differences in biological members i.e. taxonomy of organism as more broadly set forth in ‘498. In both, there are claims are directed to methods and products storing the method and a system to implement the method for each of the independent claims.
A copy of allowed claim 1 in ‘498 is provided below for comparison and completeness of the record.
A method for reducing computer memory requirements and increasing query speed to improve computational performance of a physical computer system configured to conduct taxonomic queries, comprising:
providing a database comprising k-mers of one or more organisms classified to a taxonomy, wherein the database is greater than available computer memory of a computer system;
in response to the database being greater than the available computer memory, dividing, by the computer system, the database into two or more independent groups of k-mers for at least organism A and organism B, wherein each of the groups comprises a unique set of nodes of the taxonomy, wherein all k-mers of a given node of nodes reside m only one of the groups and each of the groups is an independent data file;
assigning a taxonomic threshold level of the taxonomy, wherein the taxonomic threshold level is automatically assigned by the computer system;
providing the taxonomy as a self-consistent taxonomy that is independent of metadata associated with the k-mers from a standard taxonomy, wherein a map is generated that comprises associations of self-consistent identifications for each of the nodes in the self-consistent taxonomy to standard identifications in the standard taxonomy in response to the database being greater than the available computer memory, the self-consistent taxonomy being free of the metadata;
removing, by the computer system, k-mers common to two or more of the groups, thereby forming two or more modified groups comprising the organism A and the organism B, each of the modified groups containing a unique set of k-mers for the organism A and the organism B, each of the modified groups being an independent data file;
using, by the computer system, the k-mers of the modified groups as reference k- mers for comparison to computer queries and/or taxonomic classifications of k-mers of a sample in order to reduce query time and reduce computer storage on the available computer memory of the computer system, the sample comprising taxonomically unclassified sequenced nucleic acids of one or more organisms, wherein the computer queries and/or taxonomic classifications identifies at least one of the organisms of the sample;
generating a matrix M, wherein the matrix M includes genetic distances between genomes; and
performing a hash to determine the genetic distances, wherein the database is associated with pointers which point to rows in the database and wherein the k-mers are associated with the genomes.
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-3, 5-10, 12-16, 18-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Claim analysis
Claim 1 has been amended and still generally is directed to a computer implemented method of identifying k-mers for analyzing samples to determine biological members associated with subsets with the minimum number of k-mers. More specifically, a new step of determining k-mers and the minimum number that is necessary to determine with a ‘dictated detection sensitivity’ are recited. In view of the specification, the claims are directed to accessing sequence data to provide fragment k-mers of a target sequence which is informative to biological members and subsets within them, comparing the k-mers to sequences in a database of an associated members, for example same ‘biological member’ in a related taxonomic group set forth in the claims, and providing the assessment of which k-mers are the same between the two and which are different for use in detection method to avoid false positive or for more accurate assessment of sequence data. Additional steps have been added to claim for receiving the k-mer information and analyzing ‘the sample’ and ‘identifying’ a first subset of a biological members. No specific step or requirement is made for analyzing, and appears to encompass providing two k-mer or primer probes for informative rRNA sequences in bacteria, or k-mers for the identification of STR in CODIS and assessing the sequences of ‘the sample’ using a computer.
Dependent claims have been amended to be consistent with the independent claims and provide the sequence information is associated with an identifier and taxonomic lineage, and steps performed by the computer such as converting sequence data to binary format for k-mer ‘extraction’ from the data (claim 5), use of hash values (claim 6), using or assigning ‘origin vectors’ which can be sued to associated or distinguish possible k-mer use in analyzing other ‘biological members’ (claims 8-10). Claim 14 is directed to a ‘computer product’ that sets forth the method of claim 1 where the program instructions and a computer system provide for place and means to practice the method and set forth steps consistent with the method claims.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing sequence data to provide fragment k-mers of the sequence, comparing the k-mers to sequences in a database of an associated source, same ‘biological member’ in a related taxonomic group, and providing the assessment of which k-mers are the same between the two and which are different for use in detection method to avoid false positive or for more accurate assessment of sequence data. Dependent claims provide the sequence information is associated with an identifier and taxonomic lineage, and steps performed by converting sequence data to binary format for k-mer extraction. The steps required for the aligning and comparing sequences to arrive at k-mer sequences are instructional steps. The claim requires computing similarity scores based on hash values in dependent claims with the broad steps of receiving data and comparing it for similarity and differences. The judicial exception is a set of instructions for analysis of sequence data and appear to be directed to a Mental Processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion) for observing similarities and differences between k-mer fragments aligned to each other or a reference; and also to Mathematical Concepts, which can be mathematical calculations in providing the statistical significance of a sequence uniquely representing one taxonomic group. The breadth of “obtaining” and “determining” encompasses non-transformative visual assessment of an individual sequences and possibly associating a taxonomic significance if informative which must be in part coupled with prior knowledge of the correlation of said informative sequence for a biological member and/or taxonomic group. This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using the natural principle of associating an informative sequence with a specific use or to define a difference between taxonomic groups. Although the claims recite ‘preventing false positives’, the courts have also identified limitations that did not integrate a judicial exception into a practical application; for example, 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). Computing, constructing datasets and using statistical models was well understood, conventional, and routinely performed in the art at the time the application was filed. See MPEP § 2106.05(g) for a discussion on adding insignificant extra-solution (both pre-solution and post-solution) activity to the judicial exception. See also MPEP § 2106.05(h) for a discussion on generally linking the use of a judicial exception to a particular technological environment or field of use. The claims appear to fall into the category of Mathematical Concepts, as it applies the use of statistics and mathematical relationships in analyzing probabilities, and also into the category of mental processes, as concepts performed in the human mind (including an observation, evaluation, judgment, opinion) because there is no apparent complexity to or amount of data that is collected and analyzed as presently claimed.
Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In the instant case, the claims do not have an additional element. This judicial exception requires steps recited at high level of generality and are only stored on a non-transitory, and is not found to be a practical application of the judicial exception as broadly set forth. The claims do not recite any additional elements that integrate the judicial exception into a practical application. The claims are drawn to organizing k-mer data according to taxonomy, without a practical application.
In review of the claim limitations, the guidance of the specification and evidence of record, the judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria: an additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field; an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition; an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim; an additional element effects a transformation or reduction of a particular article to a different state or thing; or an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
For step 2B of the 101 analysis, each of the independent claims recites additional elements and are found to be the steps of obtaining sequence data. As such, the claims do not provide for any additional element to consider under step 2B. The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to: storing data on different computer nodes, storing removed data on a different computer node than modified data, and to performing a computer query or taxonomic classification using data in parallel. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because having multiple storage systems, parallel processing and cloud storage is well known, routine and convention technology. These additional elements drawn to storing the data and processing the data do not serve to meaningfully limit the abstract idea and add significantly more to the claimed process of forming k-mer groups for query and taxonomic classification. Other elements of the method include computer readable storage, and database which is a recitation of generic computer structure that serves to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry. It is noted that in explaining the Alice framework, the Court wrote that "[i]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s]ince Alice, we have found software inventions to be patent-eligible where they have made non-abstract improvements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." Viewed as a whole, these additional claim elements do not provide meaningful limitations to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claims amounts to significantly more than the abstract idea itself. Therefore, the claims are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Applicant Arguments
Applicants provide an overview for the process of the patent eligibility under 101 citing the 2019 Revised guidance and MPEP 2106, and provide a summary of the amended claims. Applicant asserts that the claim as amended is not directed to mathematical concepts noting guidance in MPEP 2106a1I.
In response, in general examiner agrees that the invention per se is not directed to mathematical concepts, however as reasoned above does or can require mathematical assessment to arrive at the determination that the k-mers represent the ‘minimum’ number of k-mers. Specifically, the claims are generic and completely relative to the breadth of ‘biological members’ and the ‘taxonomic’ range encompassed by the claims, and for example members of a human subset and members of a plant subset could likely be determined with one or two informative k-mers, whereas distinguishing between highly related bacteria which would require a statistical assessment dependent on the specificity and sensitivity (see claim 16 for example) of the final ‘identifying’ as amended. It is noted that the specification suggests that PCR or analyzing the sequence between two primers is encompassed, so assessing the sequences one to another and assessing informative variants (for example using TaxID in [0103] or more generally ‘corpus of information’ in [0114] for example) would still be relative to a statistical analysis based on a users desired outcome relative to the sample and encompasses a generic relative assessment of contig information which can be represented mathematically (see [0037]-[0048] for example).
Applicants assert that the claims do not encompass a mental process and cannot be performed by the human mind.
In response, the assertion is acknowledged but does not appear consistent with the breadth of the claims. As provided above as an example, the claims encompass any taxonomic span, and for informative k-mers to differentiate between plants and humans, using a single k-mer known to be present in a plant but not a human is encompassed by the claims and appears could be performed by observation and using the human mind. Further, for assessing sequences between or represented by two k-mer pair could also be visually assessed and performed using the human mind. Given the evidence of record, it is not clear that there is a scope which could not be visually assessed and practiced using the human mind for the claims as amended. Again, noting the requirement of the claims is all relative to the data which is to be analyzed and can encompass simple sequences, and appears to rely on the art to provide ‘the sample’ and/or assessment of k-mers relative to some sort of target representing the ‘biological members’ that may be in the sample.
Applicant provide an overview of prong 2A and argue that claims 1, 9 and 17 integrate the judicial exception (if one were still to be found) noting the claims set forth ‘physical tests… can identify biological members with a sample…’ and serves as a practical application.
In response, the claims are directed to computer implemented method and require not physical steps as asserted. Claim 14 is a computer program product and claim 19 is a system with a ‘processor set’, neither of which provide for any physical testing. Further, while the art of record and evidence suggests that generally informative k-mers can be used to analyze a sample, the claims do not require and thus is not considered a limitation of the claim nor a practical application encompassed by the claims.
Applicants argue that under step 2B that the ‘specific limitations other than what is well-understood, routine and conventional in the field…’, highlighting the fact pattern in Berkheimer v HP, Inc.
In response, Berkheimer does not appear to apply here since all the steps of the claims are directed to a judicial exception. With respect to elements not being conventional, the art and evidence appears to support that the skilled artisan readily understands that informative k-mers, primers or probes are necessary for accuracy or sensitivity of analysis methods and in part anticipate this position for the use of STR or SNP specific primers when analyzing samples. There is no evidence that the artisan would use more than needed to obtain information that was needed.
One way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
Claim 1-3, 5-10, 12-16, 18-20 rejected under 35 U.S.C. 103(a) as being unpatentable over Flygare et al. (US 2018/0365375) and Williams et al. (US 2021/0202040) is withdrawn.
In view of the amendments, the rejection using Flygare et al and Williams et al. is withdrawn.
Claim 1-3, 5-10, 12-16, 18-20 rejected under 35 U.S.C. 103(a) as being unpatentable over Klindworth et al. (2013), Chou et al. (2004), Flygare et al. (US 2018/0365375) and Williams et al. (US 2021/0202040).
Claim 1 has been amended and provides for a computer implemented method of identifying k-mers for analyzing samples to determine biological members associated with subsets with the minimum number of k-mers. More specifically, a new step of determining k-mers and the minimum number that is necessary to determine with a ‘dictated detection sensitivity’ are recited. In view of the specification, the claims are directed to accessing sequence data to provide fragment k-mers of a target sequence which is informative to biological members and subsets within them, comparing the k-mers to sequences in a database of an associated members, for example same ‘biological member’ in a related taxonomic group set forth in the claims, and providing the assessment of which k-mers are the same between the two and which are different for use in detection method to avoid false positive or for more accurate assessment of sequence data. Additional steps have been added to claim for receiving the k-mer information and analyzing ‘the sample’ and ‘identifying’ a first subset of a biological members. No specific step or requirement is made for analyzing, and appears to encompass providing two k-mer or primer probes for informative rRNA sequences in bacteria, or k-mers for the identification of STR in CODIS and assessing the sequences of ‘the sample’ using a computer. The computer product and the system of claims 14 and 20 have been amended consistently with claim 1 for implementing a computer based method.
Prior to the effective filing date method for the design of primers was well know and were provided based on the target and need of the design and use. For example Klindworth et al. provide evidence for the approach and need in the evaluation of general 16S ribosomal RNA gene and k-mers that can be used for PCR primers for classical and next-generation sequencing-based diversity studies with the taxonomic group. PCR analysis is just one possible use of a k-mer, Chou et al. is provided for additional evidence and example for the optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. As evidenced by Klindworth et al. and Chou et al. the skilled artisan could easily design and provide for necessary k-mers to provide applied analysis using the k-mers, however they do not outline the software that one can use for this analysis. However, such programs were known, for example Flygare et al. teach a database of k-mer sequences (par. 0008) from various organisms, a reference individual or source; taxonomic classification is taught (par. 0008); a Taxonomer database is taught (par. 0176)(i.e. providing a database comprising k-mers of organisms classified to a taxonomy), as in claims 1, 10, 13, 15-17. Flygare et al. teach k-mer subtraction to identify and retain k-mers that are uniquely diagnostic for a particular node or leaf in the classification database and removing k-mers that are common to multiple nodes or leaves (i.e. removing k-mers common to two or more of the groups, thereby forming two or more modified groups, each modified group containing a unique set of k-mers), as in claims 1, 10, 13 and 15.
Flygare et al. teach a threshold level used to classify reads according the taxonomic group (par. 0013)(i.e. which makes obvious assigning a taxonomic threshold level of the taxonomy), as recited in claims 10, 13 and 16. Flygare et al. teach binning k-mers in database (par. 0122) by counting unique-kmers in different taxonomic gene datasets (i.e. which makes obvious a self-consistent taxonomy which is independent of metadata). Flygare et al. teach a computer system where files of sequences are uploaded and a computer system that is remote (par. 0012); one or more computer processors are taught (par. 0015)(i.e. which makes obvious storing on different computer nodes). Flygare et al. teach a database with reference sequences used to identify microorganisms (par. 0064)(i.e. which makes obvious using a set of removed k-mers to confirm identification of an organism). Flygare et al. teach bacteria, viruses, and fungi at least (par. 0008). Flygare et al. suggest a medical sample by teaching a sample from an individual with a condition needing treatment (par. 0009). Flygare et al. teach parallel sequence comparison may comprise comparison with sequences from two or more different taxonomic groups (par. 0070)(i.e. which makes obvious a parallel computer query of taxonomic classification).
Flygare et al. teach classifying the sequencing read as belonging to a second taxonomic group that is more specific than the first taxonomic group if a measure of similarity between the sequencing read and reference sequence is above a first threshold level and if no similarity exists (i.e. assign a taxonomic threshold level of the taxonomy, wherein it would be obvious to remove k-mers above the threshold level). Flygare et al. teach plasmids (par. 0046 and 0081) which are mobile elements as described in the instant specification (page 8, line 5) wherein it would be obvious to remove data not part of the taxonomy. Flygare et al. does not specifically teach the limitation of claims 1, 10, 13 and 15-17 reciting dividing the database into independent groups of k-mers wherein each group comprises a unique set of nodes of the taxonomy wherein all k-mers of a given node reside in only one of the groups. Flygare et al. does not specifically teach the limitation of claims 1, 10, 13 and 15 reciting that the modified groups are capable of serving as reference k-mers for computer queries or taxonomic classification of k-mers of a sample comprising taxonomically unclassified sequenced nucleic acids of one or more organisms. Under the standard of Broadest Reasonable Interpretation, this limitation is an intended use.
Flygare et al. also does not specifically teach organizing the data into a hierarchal node of information. However, Williams et al. teach (Figure 2) information in a k-mer database grouped according to different species and different species in a hierarchical node formation (Figure 4)(i.e. dividing the database into independent groups of k-mers wherein each group comprises a unique set of nodes of the taxonomy wherein all k-mers of a given node reside in only one of the groups). Williams et al. teach a hash table which is a k-mer database used in computer queries to classify reads into species (par. 0120-0121)(i.e. groups of k-mers serving as computer queries or taxonomic classification of k-mers of a sample comprising taxonomically unclassified sequenced nucleic acids of one or more organisms). Williams et al. teach whenever a new k-mer occurs, a new space is allocated to the hash table and a unique numerical ID is stored (par. 0090)(i.e. taxonomy is based on genetic distances, the genetic distances are genome-genome distances calculated using the MinHash algorithm). Williams et al. teach KRAKEN that performs an exact match comparison of a database of reference bacterial genes, matches reads and selects a higher taxonomic rank if an exact match between two different species exists (par. 0100 and 0119)(i.e. which suggests a threshold level from a species and selecting a taxonomic threshold level by a machine using artificial intelligence). Williams et al. teach EzBioCloud database (par. 0105). Given the detailed description of both Flygare et al. and Williams et al. it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to combine the well known teachings of both Flygare et al. and Williams et al. to combine and substitute to conclude that the combination of the references represents a combination of known elements which yield the predictable result. At the time of invention, a practitioner could have combined the method of taxonomic classification where shared sequences are removed, as taught by Flygare et al. with the teaching of Williams to group different species in a database arranged as a hierarchical set of nodes. The result would amount to the instantly claimed process of dividing k-mers in a database by independent groups and removing k-mers common to two or more groups. Such a combination is merely a "predictable use of prior art elements according to their established functions." KSR Int’l 7, 127 S. Ct. at 1740. Thus, the claimed invention as a whole was clearly prima facie obvious.
Response to Applicants arguments
To the extent the arguments apply to the new rejection Applicants argue that conclusionary statements cannot sustain a legal conclusion of obviousness and note limitations of the newly amended claims. Applicants argue that neither Flygare nor Williams teach using a processor to achieve a dictated sensitivity with a minimum number of k-mers.
In response, Flygare and Williams were used to support that software and computer approaches for assessing whether a k-mer was homologous to one or more sequences in a database were known, and given the generality of the claim for computer implementation using a processor or for instructions on a media, could be used for exact match to demonstrate sensitivity and accuracy that might be achieved for the design of a k-mer. Klindworth et al. and Chou et al. have been provided to demonstrate such applications known in the art for the use of k-mers, and more specifically for providing the analysis and approach for the design and use of the k-mers for various targets of interest and ones capable of distinguishing taxonomic differences. As outlined in the analysis of the amended claims, there is no specific target required only the analysis of any possible targets to arrive at k-mers that can distinguish between members in a group which both Klindworth et al. and Chou et al. provide. Using ‘one or more computer processors’ for each of the steps broadly provides for doing the analysis using a computer which Klindworth et al. and Chou et al. provide generally, but Flygare and Williams demonstrate.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R Skowronek can be reached on 571 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Joseph Woitach/ Primary Examiner, Art Unit 1687
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