Response to Amendment
The amendment filed on December 10, 2025 has been entered. Claims 1 and 12 have been amended, and claims 7, 8, 14 have been canceled. Claims 1-6, 9-13, 15 are currently pending in the application.
Response to Arguments
35 U.S.C 103
Applicant’s arguments filed with respect to the rejection(s) of claims 1-15 under U.S.C 103 have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However upon further consideration, new grounds of rejection are made in view of Shukla (U.S Pub # 20150213079).
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
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/TONY WU/ Primary Examiner, Art Unit 2166