Response to Arguments
35 U.S.C 103
Regarding independent claims 1-6, 9-13, 15, Applicant argues that Shukla does not discloses “(ii) analytics information detailing a source dataset and one or more processing steps for producing the genomic dataset, wherein the analytics information comprises instructions for verification of data reproducibility by evaluating a concordance of the genomic dataset with an existing counterpart genomic dataset being verified”.
Examiner has carefully considered Applicant’s argument and respectfully disagrees. In response to the preceding argument examiner respectfully submits that Shukla discloses the above limitations. Examiner interprets from Shukla in paragraph 78 “The method includes requesting, by the first computing device, from a second computing device, a first verification output derived from at least one first input based upon a first set of omic data maintained by the second computing device (304). The method includes receiving, by the first computing device and from the second computing device, the first verification output (306). The method includes determining, by the first computing device, that the first verification output matches the first set of verification data (308). The method includes directing, by the first computing device, the calculation of a matching score, by the second computing device and a third computing device, by means of a secure multiparty computation using the at least one first input and at least one second input based upon a second set of omic data maintained by the third computing device, responsive to the determination that the first verification output matches the first set of verification data”, instructions to verify a first set of omic data with a first verification output derived from the first set of omic data. The claims state that the genomic dataset is verified with a counterpart genomic dataset however a counterpart genomic dataset does not explicitly state that a counterpart genomic dataset is the exact same dataset. In this example from Shukla, a verification output is derived from the first genomic data set is compared to the first genomic dataset. This verification output includes calculating a matching by means of a secure multiparty computation. Thus in this example Shukla discloses “instructions for verification of data reproducibility by evaluating a concordance of the genomic dataset with an existing counterpart genomic dataset being verified” by checking whether a verification output of initial omic data input matches the initial omic data input.
Further regarding claim 1, Applicant argues that there is no reasonable motivation to modify ISO by Shukla nor Cotton.
Examiner has carefully considered Applicant’s argument and respectfully disagrees. Examiner reiterates that analyzing user’s genomic data requires a great deal of privacy and trust. Shukla provides several reasons such as ([0005] to preserve privacy in genomic transactions is to utilize combinations of data encryption and computational techniques in order to enable calculations on genomic data, without revealing the entirety of that genomic data to any one party) and ([0006] enable individuals to perform computations on encrypted data, without decrypting the data, thereby yielding a computationally sound result of a calculation without disclosing the input data) for privacy-preserving computation on genomic information. A person’s genomic information is their identity and keeping personal identity information protected from third party analysts would be a reasonable motivation to modify the system of ISO by Shukla. Similarly with Cotton, Cotton is used to disclose teaching a system to facilitate data traceability and an access history. The motivation provided to modify ISO and Shukla by Cotton ([0012] allow a scientific user to access, manage and analyze integrated scientific data from a variety of external and internal databases) is a perfectly reasonable motivation to provide communication between different scientific users belonging to different organizations to access and analyze genomic data from different locations. Given the above, the examiner maintains the rejection in view of ISO, Shukla and Cotton.
Claim Rejections - 35 USC § 103
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 1-5, 9-13, 15 are rejected under 35 U.S.C. 103 as being unpatentable over Text of ISO/IE CD 23092-6 Coding of Genomic Annotations (Motion Picture Expert Group or ISO/IEC JTC1/SC29/WG11) hereby to referred to as ISO that was submitted in an IDS filed on 03/23/2023 in view of Shukla (U.S Pub # 20150213079) and in further view of Cotton (U.S Pub # 20030187821).
With regards to claim 1, ISO discloses a method for storing genomic data within a data structure comprising a file structure, the method comprising:
receiving a genomic dataset comprising a plurality of fields or attributes of different data types ([Introduction, page 8 lines 4-8] genomic record including different data types);
generating an information metadata structure for the genomic dataset, comprising one or more of: (i) information about an annotation table within the file structure, including one or more user profiles and associated profile permission; ([Section 7.3.2, Section 7.3.5, Page 33, Page 36] annotation__table_protection that describes access control policy enforcement for users)
(ii) analytics information detailing a source dataset and one or more processing steps for producing the genomic dataset, wherein the analytics information is configured to facilitate verification of data reproducibility ([Section 7.3.2, Section 7.3.6, Page 33, Page 37]);
(iv) linkage information defining a relationship between the annotation table and one or more data objects, wherein the linkage information is configured to enhance data navigation and/or to support a data query across linked data ([Section 7.3.2, Section 7.3.6, Page 33, Page 37]) annotation table indices consist of one or multiple indexing data structures that support query on the annotation data;
compressing the genomic data, and the information metadata, using one or more compression algorithms to generate a compressed genomic dataset and compressed information metadata; and storing the compressed genomic dataset and the compressed information metadata in a container data structure ([Introduction Page 10, Section 8.4.4 Page 78 compressor parameter set] compress genomic sequencing and annotation table);
wherein some or all of the annotation table is encrypted ([Section 7.3.5.2 Page 36] encryption).
ISO does not disclose however Shukla discloses:
wherein the one or more user profiles can be created by a user, encrypted for confidentially, signed for authenticity, and/or shared with another designated user ([0049] encrypt users omic data);
(ii) analytics information detailing a source dataset and one or more processing steps for producing the genomic dataset ([0049] genomic analyses), wherein the analytics information comprises instructions for verification of data reproducibility by evaluating a concordance of the genomic dataset with an existing counterpart genomic data being verified ([0049] Genomic analyses for verifying data integrity and authenticating data provenance. An authentication server using the disclosed implementations can at once guarantee that both parties to the calculation are using genuine and un-tampered-with omic data, and that the authentication server itself cannot intentionally or unintentionally violate the privacy of either party. [0078] determining, by the first computing device, that the first verification output matches the first set of verification data);
It would have been obvious for one of ordinary skill in the art before the date the current invention was effectively filed to have modified ISO by Shukla to use verification results to verify a genomic data set.
One of ordinary skill in the art would have been motivated to make this modification in order to maintain genetic information private from other people (Shukla [0003]).
Cotton discloses:
(iii) access history for the genomic dataset, configured to facilitate data traceability, wherein the verification of the data reproducibility includes verifying the authenticity and/or integrity of the access history ([0159] The traceability feature is particularly important for responding to the FDA, for example, or in any other report where the entity reported to requires a complete verification of the data gathered and its history from time of entry into the system. By selecting which artifact should be traced, (i.e., by selecting the unique identifier of the artifact to be traced) all events with have been generated, and hence, linked to that unique identifier are produced in chronological order, giving a complete history of who entered the data and when and as to how the data has been further developed, used, commented on, revised, etc. up to the time that the traceability report is produced).
It would have been obvious for one of ordinary skill in the art before the date the current invention was effectively filed to have modified ISO and Muse by the system of ISO to produce a traceability report.
One of ordinary skill in the art would have been motivated to make this modification in order to allow a scientific user to access, manage and analyze integrated scientific data from a variety of external and internal databases (Cotton [0012]).
Claim 12 corresponds to claim 1 and is rejected accordingly.
With regards to claim 2, ISO further discloses:
further comprising the steps of: receiving new data for the annotation table; and updating the annotation table, comprising updating one or both of the information metadata and the genomic data ([Section 7.3.2 Page 30] annotation table).
Claim 13 corresponds to claim 2 and is rejected accordingly.
With regards to claim 3, ISO further discloses:
wherein one or more of (i) through (iv) comprise selective encryption and a digital signature ([Section 7.3.5.2 Page 36] selective encryption and signature).
With regards to claim 4, ISO further discloses:
wherein the access history for the genomic dataset is configured to track access and/or change to the genomic data by one or more users, and wherein tracked access or changes are predefined ([Section 7.3.5.2 Page 36] privacy rules specify who can execute a given action and under which condition according to XACML).
With regards to claim 5, ISO further discloses:
([Section 7.3.5.2 Page 36] privacy rules specify who can execute a given action and under which condition according to XACML).
With regards to claim 9, ISO further discloses:
with an optional digital signatures by a user that performed the verification ([Section 7.3.5.2 Page 36] selective encryption and signature).
ISO does not disclose however Shukla discloses:
wherein the analytics information further comprises one or more verification results ([0078] verification output).
It would have been obvious for one of ordinary skill in the art before the date the current invention was effectively filed to have modified ISO by Shukla to use verification results to verify a genomic data set.
One of ordinary skill in the art would have been motivated to make this modification in order to maintain genetic information private from other people (Shukla [0003]).
With regards to claim 10, ISO further discloses:
wherein the linkage information comprises one or more specifications for mapping data between one or more annotation tables ([Section 7.3.1 Page 32-33] linkage information).
With regards to claim 11, ISO does not disclose however Newman discloses:
verifying data reproducibility using the analytics information and ([0159] verification of the data gathered and its history).
It would have been obvious for one of ordinary skill in the art before the date the current invention was effectively filed to have modified ISO and Muse by the system of ISO to produce a traceability report.
One of ordinary skill in the art would have been motivated to make this modification in order to allow a scientific user to access, manage and analyze integrated scientific data from a variety of external and internal databases (Cotton [0012]).
Claim 15 corresponds to claim 10 and is rejected accordingly.
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Text of ISO/IE CD 23092-6 Coding of Genomic Annotations (Motion Picture Expert Group or ISO/IEC JTC1/SC29/WG11) in view of Shukla (U.S Pub # 20150213079) and in further view of Cotton (U.S Pub # 20030187821) and Adams (U.S Pub # 20140115515).
With regards to claim 6, ISO does not disclose however Adams discloses:
wherein the one or more user profiles comprise one or more parameters for presentation and/or further processing such as filtering, sorting, and/or highlighting of the genomic data ([0067] The display is user controllable in the sense that (depending on how the system is configured), the user may request one or more of the following in any combination: a change in expansion or detail, the imposition or removal of filters, highlighting or annotating a particular variant identified by the system or a gene region comprising one or more variations of interest, and permitting other system users to provide their own annotations directly on the display).
It would have been obvious for one of ordinary skill in the art before the date the current invention was effectively filed to have modified ISO, Shukla and Cotton by the system of Adams to allow a user to customize how they want to visualize genomic data.
One of ordinary skill in the art would have been motivated to make this modification in order to display variations between genomes between different individuals of the same species (Adams [0006]).
Conclusion
THIS ACTION IS MADE FINAL. 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 TONY WU whose telephone number is (571)272-2033. The examiner can normally be reached Monday-Friday (9-5).
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/TONY WU/ Primary Examiner, Art Unit 2166
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