DETAILED ACTION
The Applicant’s filing, received 30 June 2022, has been fully considered. The following rejections and/or objections constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
There were two sets of claims received 30 June 2022. The set of claims without the header information “WO 2021/138218” and “PCT/US2020/067003” is the set of claims that have been examined herein.
Claims 1-14 are pending.
Claims 1-3, 6, 9, 11, and 12 are rejected.
Claims 4, 5, 7, 8, 10, 13, and 14 are objected to.
Priority
This application is a 371 of PCT/US20/67003, filed 24 December 2020, which claims benefit of priority to U.S. Provisional Application No. 62/956,729, filed 03 January 2020.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Therefore, the effective filing date of the claimed invention is 03 January 2020.
Drawings
There were two sets of drawings received 30 June 2022. The set of drawings without the header information “WO 2021/138218” and “PCT/US2020/067003” is the set of drawings that have been accepted.
Specification
There were two Specifications received 30 June 2022. The Specification without the header information “WO 2021/138218” and “PCT/US2020/067003” is the Specification that has been accepted.
Information Disclosure Statement
The information disclosure statements (IDS) received 30 June 2022 and 01 May 2023 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner.
Claim Interpretation
Claim 1 recites the limitation “storing bacterial infection/contamination data in a spatio-temporal infection database, in which the data is derived from bacterial isolates from one or more treatment locations.” This limitation is interpreted as a product-by-process limitation, with the product being the data stored in the database (i.e., the bacterial infection/contamination data) and further interpreted as not requiring the active steps of performing the process of generating the bacterial infection/contamination data.
Claim Objections
Claims 4, 5, 7, 8, 10, 13, and 14 are objected to under 37 CFR 1.75(c) as being in improper form because a multiple dependent claim should refer to other claims in the alternative only. See MPEP § 608.01(n).
Accordingly, these claims have not been further treated on the merits.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 6 and 9 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 6 and 9 contain the trademark/trade name “PhageScore.” Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name “PhageScore” is used to identify/describe a quantitative, mathematical method used to evaluate and compare the lytic activity (killing efficiency) of different bacteriophages against hosts (e.g., paras. [0056] & [0057] in the Specification) and, accordingly, the identification/description is indefinite.
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, 6, 9, 11, and 12 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter?
Claims 1-3, 6, and 9 recite a method of selecting a phage formulation (i.e., a process); Claim 11 recites a method of treating a patient (i.e., a process); and claim 12 recites a method of treating a surface (i.e., a process).
Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
at least one of the following data fields: (1) a clinical indication, (2) a bacteria identification, (3) a clinical outcome, (4) a phage resistance status, (5) a phage susceptibility profile, (6) an antibiotic susceptibility profile, and/or (7) a lab test result relating to any one of (1)-(6) (i.e., mental processes);
identifying one or more phage suitable for inclusion in the phage formulation by analyzing the data fields of (1)-(7) to identify to one or more infections associated with a treatment location during a historical time period based at least on one or more of a frequency of infections/contamination, a geographic clustering of infections/contamination, and/or phage usage data (i.e., mental processes); and
generating a selected list of one or more phage(s) to be included in the phage formulation (i.e., mental processes).
Independent claim 11 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
at least the abstract ideas recited by independent claim 1 (i.e., mental processes); and
a PhageScore higher than one standard deviation from the mean (i.e., mental processes and mathematical concepts).
Independent claim 12 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
at least the abstract ideas recited by independent claim 1 (i.e., mental processes); and
a PhageScore higher than one standard deviation from the mean (i.e., mental processes and mathematical concepts).
Dependent claims 2, 3, 6, and 9 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 2 further recites:
the data field comprising the bacteria identification is defined by genus, species, strain, sequence, and/or NCBI tax ID (i.e., mental processes).
Dependent claim 3 further recites:
repeating the identification step for a more recent historical time period and repeating the generating step if there is a change to the one or more phage identified as suitable for inclusion in the therapeutic phage formulation (i.e., mental processes).
Dependent claim 6 further recites:
the phage identified as having a PhageScore above one standard deviation from the mean is added to the selected list (i.e., mental processes and mathematical concepts).
Dependent claim 9 further recites:
the phage inventory management system is updated with new phage having a PhageScore higher than one standard deviation from the mean (i.e., mental processes and mathematical concepts).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., generating a selected list of one or more phage(s) to be included in the phage formulation), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., the phage identified as having a PhageScore above one standard deviation from the mean is added to the selected list) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 1-3, 6, 9, 11, and 12 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Dependent claims 2, 6, and 9 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claim 1 include:
storing bacterial infection/contamination data in a spatio-temporal infection database, in which the data is derived from bacterial isolates from one or more treatment locations.
The additional elements in independent claim 11 include:
storing bacterial infection/contamination data in a spatio-temporal infection database, in which the data is derived from bacterial isolates from one or more treatment locations (i.e., the phage formulation of claim 10 requires the additional elements recited by claim 1); and
administering to the patient the phage formulation.
The additional elements in independent claim 12 include:
storing bacterial infection/contamination data in a spatio-temporal infection database, in which the data is derived from bacterial isolates from one or more treatment locations (i.e., the phage formulation of claim 10 requires the additional elements recited by claim 1); and
treating a surface with the phage formulation.
The additional element in dependent claim 3 includes:
updating the database with additional infection-related data.
The additional elements of storing bacterial infection/contamination data in a spatio-temporal infection database, in which the data is derived from bacterial isolates from one or more treatment locations (claims 1, 11, and 12); and updating the database with additional infection-related data (claim 3); invoke a computer and/or computer-related components (i.e., a database) merely as tools for use in the claimed process, and therefore are not an improvement to computer functionality itself, or an improvement to any other technology or technical field, and thus, do not integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(1)).
The additional elements of administering to the patient the phage formulation (claim 11) and treating a surface with the phage formulation (claim 12); do not apply or use the recited judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition (i.e., at the very least, factor (a.) at MPEP 2106.04(d)(2) is not satisfied), and therefore the application or use of the judicial exception in this manner does not meaningfully limit the claims by going beyond generally linking the use of the judicial exception to a particular technological environment (e.g., treatment of bacterial infections and/or bacterially contaminated surfaces).
Thus, the additionally recited elements merely invoke a computer and/or computer related components as tools; and/or a field of use in which to apply a judicial exception; and/or do not effect a particular treatment or prophylaxis for a disease or medical condition; and as such, when all limitations in claims 1-3, 6, 9, 11, and 12 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-3, 6, 9, 11, and 12 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Dependent claims 2, 6, and 9 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claims 1, 11, and 12 and dependent claim 3 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 storing data in a database (claims 1, 11, and 12) and updating information in a database (claim 3); are conventional computer components and/or functions (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The additional elements of administering to the patient the phage formulation (claim 11) and treating a surface with the phage formulation (claim 12); are conventional. Evidence of conventionality is shown by:
Gordillo Altamirano et al. (“Phage Therapy in the Postantibiotic Era.” Clinical Microbiology Reviews, (2019), Vol. 32, Issue 2, pp. 1-25); and
Fernandez et al. (“Bacteriophages in the Dairy Environment: From Enemies to Allies.” Antibiotics, (2017), Vol. 6, No. 27, pp. 1-14).
Gordillo Altamirano et al. reviews the therapeutic use of bacteriophages, i.e., viruses that infect and kil bacteria, and shows that these therapies are well suited to be part of the multidimensional strategies to combat antibiotic resistance (Abstract) and further shows a timeline of major events in the history of research on phages, phage therapy, and antibiotics (Figure 1).
Fernandez et al. reviews the use of bacteriophages in the dairy environment (Abstract) and shows the use of phages as disinfectants and preservatives (Section 4.1); and further shows principal points of disinfection and biocontrol along the dairy chain where phages can be applied to ensure dairy safety (Figure 3; e.g., food-contact surfaces); and further shows a commercial phage-based product for use as a disinfectant for food facilities and also on cheese surfaces (page 8, para. 2).
Therefore, when taken alone, all additional elements in claims 1-3, 6, 9, 11, and 12 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-3, 6, 9, 11, and 12 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.
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.
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.
Claims 1-3, 11, and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Harper (“Criteria for Selecting Suitable Infectious Diseases of Phage Therapy.” Viruses, (2018), Vol. 10, No. 177, pp. 1-11) in view of Alcock et al. (“CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.” Nucleic Acids Research, (2020), Vol. 48, Database issue, pp. D517-D525) in view of Russell et al. (“PhagesDB: the actinobacteriophage database.” Bioinformatics, (2017), Vol. 33(5), pp. 784-786).
Independent claims 1, 11, and 12 are broadly directed to using bacterial infection/contamination data stored in a database to identify one or more phage suitable for inclusion in a phage formulation for use as a therapeutic and/or disinfectant, and presenting the one or more identified phage in a list of suitable phage for inclusion in the phage formulation.
Dependent claims 2 and 3 further define the database, i.e., the data fields that are included in the database (claim 2) and a step of updating the database with more recent data and generating a revised updated list of identified phages (claim 3).
Harper discusses the importance of selecting appropriate infectious disease targets for phage therapy (Title) and further discusses the highly specific nature of bacteriophages and of their mechanisms of action, and therefore the importance of considering factors such as the characteristics of the infection to be treated, the characteristics of the bacteria involved, and the characteristics of the bacteriophages themselves (Abstract).
Alcock et al. discusses the surveillance of the antibiotic resistome using a comprehensive antibiotic resistance database (i.e., CARD - Comprehensive Antibiotic Resistance Database) that is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (i.e., AMR).
Russell et al. discusses an actinobacteriophage database called PhagesDB, which is a comprehensive, database-backed website that collects and shares information related to the discovery, characterization and genomics of viruses that infect Actinobacterial hosts, including more than 8,000 bacteriophages (Abstract).
Regarding independent claims 1, 11, and 12, Harper shows relevant steps in a process for determining a bacterial pathology for bacteriophage therapy and selecting suitable bacteriophages (page 7, Figure 2).
Regarding independent claims 1, 11, and 12, Harper does not show using a spatio-temporal database with bacterial infection/contamination data and/or bacteriophage data; and further does not show generating a list of phages suitable for inclusion in a phage formulation for therapeutic/disinfectant use.
Regarding independent claims 1, 11, and 12, Alcock et al. shows a comprehensive antibiotic resistance database (i.e., CARD - Comprehensive Antibiotic Resistance Database) that is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (Abstract).
Regarding independent claims 1, 11, and 12, Harper in view of Alcock et al. does not show a spatio-temporal database with bacteriophage data, or identifying one or more phage suitable for inclusion in a phage formulation, or generating a selected list of the one or more suitable phages.
Regarding independent claims 1, 11, and 12, Russell et al. shows a comprehensive, interactive, database-backed website with over 8,000 bacteriophages (Abstract) and further shows that the database has a variety of ways that the user can view and interact with phage groups, in particular phage lists can be generated and sorted by host (genus, species, or strain), cluster, subcluster, institution, year found, genome length, G + C content, and several other criteria, and that the filter page allows for combining criteria to target a group of phages with specific characteristics (page 785, col. 1, para. 2); and further shows that each phage cluster and subcluster has its own page with a list of member phages as well as meta-data about the cluster/subcluster itself, such as number of members and the host genera which its members infect (Ibid.); and further shows that there is an interactive map that displays all sequenced phages/clusters with known GPS coordinates, which provides information about the geographical distribution of phage isolation locations (Ibid.).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method shown by Harper by incorporating methods for using a database of bacteria, as shown by Alcock et al., and discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Harper with the methods of Alcock et al. because Alcock et al. shows a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (Abstract). This modification would have had a reasonable expectation of success given that both Harper and Alcock et al. are directed to bacterial infectious diseases.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method shown by Harper in view of Alcock et al. by incorporating methods for a comprehensive, interactive, database-backed website that collects and shares information related to viruses that infect bacteria, as shown by Russell et al., and discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Harper in view of Alcock et al. with the methods of Russell et al., because Russell et al. shows methods for archiving and updating phage information in a database that can then be accessed and sorted and filtered in various ways to target a group of phages with specific characteristics, e.g., geographical distribution and the host genera which a particular group of phages infects, and further motivated to use the targeted phages for therapeutic/disinfectant purposes. This modification would have had a reasonable expectation of success given that both Harper in view of Alcock et al. and Russell et al. disclose related methods useful for addressing bacterial infectious diseases, e.g., using curated information repositories to characterize pathologies and identify bacteriophages with suitable lytic activity.
Regarding dependent claims 2 and 3, Russell et al. further shows multiple database fields for storing different data (Ibid.) (claim 2) and further shows that the database is routinely updated (page 785, col. 1, para. 4) and was designed to be synchronized with the pace of discovery (page 785, col. 2, para. 4) (claim 3).
Thus, the claims were prima facie obvious.
Claims 6 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Harper in view of Alcock et al. in view of Russell et al. as applied to claims 1-3, 11, and 12 above, and further in view of Bourdin et al. (“Coverage of diarrhoea-associated Escherichia coli isolates from different origins with two types of phage cocktails.” Microbial Biotechnology, (2014), Vol. 7, pp. 165-176).
Harper in view of Alcock et al. in view of Russell et al. as applied to claims 1-3, 11, and 12 above, do not explicitly show a mathematical equation for calculating a score for representing the lytic activity of different bacteriophages.
Dependent claims 6 and 9 further define the ranking of phages according to a score.
Bourdin et al. discusses the use of different phage cocktails against different bacteria isolates from different geographical regions (Title; and Abstract) and shows assigning lysis scores to a phage added at three different multiplicities of infection (MOI, i.e., the ratio of infectious phage particles (PFU) to target bacterial cells (CFU)) (Fig. 1).
Regarding dependent claims 6 and 9, Bourdin et al. shows assigning a lysis score (i.e., lytic activity (killing efficiency)) for a phage against a pathogenic E. coli strain (Fig. 1).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method shown by Harper in view of Alcock et al. in view of Russell et al. as applied to claims 1-3, 11, and 12 above, by incorporating methods for assigning killing efficiency scores to phages based on their lytic activity against bacterial strains, as shown by Bourdin et al., and discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Harper in view of Alcock et al. in view of Russell et al. as applied to claims 1-3, 11, and 12 above, with the methods of Bourdin et al., because Bourdin et al. shows methods for scoring the lysis activity of a phage based on killing efficiency against a bacterial strain, and further motivated to model the lytic activity mathematically using an equation in order to spare the time and expense of laboratory experiments. This modification would have had a reasonable expectation of success given that both Harper in view of Alcock et al. in view of Russell et al. as applied to claims 1-3, 11, and 12 above, and Bourdin et al. disclose methods for identifying bacteriophages.
Thus, the claims were prima facie obvious.
Conclusion
No claims are allowed.
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this application.
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687