DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
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 1-18 are rejected under 25 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1
Claims 1-18 are within the four statutory categories. However, as will be shown below, claims 1-18 are nonetheless unpatentable under 35 U.S.C. 101.
Claim 1 is representative of the inventive concept and recites:
A system for collecting, displaying, and modeling a patient medical record, comprising:
a processor; a main memory in communication with the processor via a communication infrastructure, said memory including stored instructions that, when executed by said processor, cause said processor to:
access an electronic health record including clinical data corresponding to a patient, the clinical data normalized to a Fast Healthcare Interoperability Resources (FHIR) format;
analyze the clinical data to create a problem list including one or more medical diagnoses associated with the patient;
retrieve, via one or more FHIR genomic operations, genomic data corresponding to the patient, wherein said genomic data is stored in a genomic server, said genomic server configured to interface with the electronic health record, wherein executing the one or more FHIR genomic operations comprises performing server-side normalization of variant data and genomic liftover across heterogeneous reference assemblies;
generate a digital twin based on the problem list, the clinical data, and the genomic data;
output said digital twin to a user, wherein said digital twin includes interactive components corresponding to at least one of a genome, clinical condition, treatment, and clinical trial;
receive, from the user, a user query via the interactive components;
query, using one or more FHIR phenotype operations, the genomic data and the clinical data based on the user query;
and receive at least one of a diagnostic implication and therapeutic implication for the patient as output from the one or more FHIR phenotype operations.
*Claim 10 recites similar limitations as claim 1, but for a method
Step 2A Prong One
The broadest reasonable interpretation of these steps includes mental processes because the
highlighted components can practically be performed by the human mind (in this case, the process of
analyzing and generating) or using pen and paper. Other than reciting generic computer components/functions such as “processor” and “main memory in communication with the processor”, and “stored instructions”, nothing in the claims precludes the highlighted portions from practically being performed in the mind. For example, in claim 1, but for the generic computer language, the claim encompasses the user collecting data, processing it, and then making prediction based on the analysis of data. If a claim limitation, under its broadest reasonable interpretation, cover performance of the limitation in the mind but for the recitation of generic computer components/functions, then it falls within “Mental Processes” grouping of abstract ideas. Additionally, the mere nominal recitation of a generic computer does not take the claim limitation out of the mental process grouping. Thus, the claim recites a mental process. The recitation of generic computer components/functions of retrieving, and receiving also covers behavioral or interactions between people (i.e. a computer and user interface), and/or managing personal behavior or relationships or interactions between people (i.e. social activities, teaching, and following rules or instructions – in this case a person is able to physically follow the steps to collect and analyze data), hence the claim falls under “Certain Methods of Organizing Human Activity”.
Dependent claims 2-9 and 11-18 recite additional subject matter which further narrows or
defines the abstract idea embodied in the claims (such as claim 2, reciting what types of data that clinical data entails, but for recitation of generic computer components/functions).
Step 2A Prong Two:
This judicial exception is no integrated into a practical application. In particular, the claims recite the
following additional limitations:
Claim 1 recites: “processor”, “main memory in communication with the processor”, and “stored instructions”, “digital twin”, “output said digital twin to a user, wherein said digital twin includes interactive components corresponding to at least one of a genome, clinical condition, treatment, and clinical trial”, “receive, from the user, a user query via the interactive components”, and “query, using one or more FHIR phenotype operations, the genomic data and the clinical data based on the user query”, and “wherein said genomic data is stored in a genomic server, said genomic server configured to interface with the electronic health record, wherein executing the one or more FHIR genomic operations comprises performing server-side normalization of variant data and genomic liftover across heterogeneous reference assemblies”
In particular, the additional elements do no integrate the abstract idea into a practical application, other
than the abstract idea per se, because the additional elements amount to no more limitations which:
Amount to mere instructions to apply an exception (MPEP 2106.05(f)). The limitations of
are recited as being performed by a “processor”, “main memory in communication with the processor”, “stored instructions”, and “wherein said genomic data is stored in a genomic server, said genomic server configured to interface with the electronic health record”. A computer is recited at a high level of generality and amounts to no more than mere instructions to apply the exception using a generic computer.
Add insignificant extra-solution activity (MPEP 2106.05(g)) to the abstract idea such as the
recitation of “digital twin”, “output said digital twin to a user, wherein said digital twin includes interactive components corresponding to at least one of a genome, clinical condition, treatment, and clinical trial”, “receive, from the user, a user query via the interactive components”, and “query, using one or more FHIR phenotype operations, the genomic data and the clinical data based on the user query”, and “wherein said genomic data is stored in a genomic server, said genomic server configured to interface with the electronic health record, wherein executing the one or more FHIR genomic operations comprises performing server-side normalization of variant data and genomic liftover across heterogeneous reference assemblies”.
Dependent claim 8 recites “output”
Dependent claim 17 recites “output”
In particular, the additional elements do no integrate the abstract idea into a practical application, other
than the abstract idea per se, because the additional elements amount to no more limitations which:
Add insignificant extra-solution activity (MPEP 2106.05(g)) to the abstract idea such as the
recitation of “output”.
Dependent claims 2-7, 9, 11-16, and 18 do not include any additional elements beyond those
already recited in independent claims 1 and 10 and dependent claims 8 and 17, and hence do not integrate the aforementioned abstract idea into a practical application. Looking at the limitations as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or any other technology. Their collective function merely provides conventional computer implementation and do not impose a meaningful limit to integrate the abstract idea into a practical application.
Step 2B
Claims 1 and 10 do not include additional elements that are sufficient to amount to significantly
more than the judicial exception. As discussed above with respect to discussion of integration of the
abstract idea into a practical application, the additional elements: A system in claim 1; amount to no
more than mere instructions to apply an exception to the abstract idea. Additionally, the additional
limitations, other than the abstract idea per se, amount to no more than limitations which amount to
elements that have been recognized as well-understood, routine, and conventional activity in particular
fields as demonstrated by the recitation of:
Digital twin (claims 1 and 10), which is a virtual representation of a physical asset, process, and system that is linked to its real-world counterpart in a manner that would be well-understood, routine, and conventional.
Para 0039, Milev(US20190260831A1) discloses: “The cloud platform 220 may also host conventional digital twins.”
Para 0017, Bohm(US20200274768A1) discloses: “It is conventional in such a procedure to already develop a digital twin for these systems in the design phase since typically all systems are actually not yet physically present in this design phase.”
Para 0039, Falk(US 20210081938 A1) discloses: “In particular, by contrast, further data, in particular with a high data volume and high change frequency, can be stored in a conventional digital twin (e.g., the primary digital twin).”
Outputting (claims 1, 8, 10, and 17), which refers to the process of transmitting or sending data from a computer or other system to another destination, such as a display, a storage device, or another computer system ( TLI Communications LLC v. AV Auto. LLC, 823 F.3d 607, 614, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) ) in a manner that would be well-understood, routine, and conventional.
Generate a digital twin (digital twinning), which refers to the creation of virtual, real-time replicas of physical objects, processes, or systems (Para 0102, Mukherjee discloses: “Consumption graphs 603 and 601 show that the datacenter consumes more power using conventional digital twinning methods compared to using edge-node digital twinning methods.”) in a manner that would be well-understood, routine, and conventional.
Receiving (claims 1 and 10), which refers to taking take in, download, or accept information from another source(TLI Communications LLC v. AV Auto. LLC, 823 F.3d 607, 610, 118 USPQ2d 1744, 1745 (Fed. Cir. 2016)) in a manner that would be well-understood, routine, and conventional.
Querying (claims 1 and 10), which refers to a request for data in a database (Para 0081, Liang(US 20190180186 A1) discloses: “In one implementation, the genomes in candidate genome pool database 902 are stored and managed by conventional database management systems (DBMS), and are accessed using SQL statements. Thus, a conventional SQL query can be used to obtain, for example, the fitness function 904 of the genomes.”) in a manner that would be well-understood, routine, and conventional.
Storing (claims 1 and 10), which refers to the technology-driven process of capturing, retaining, and managing digital information on physical or virtual media (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015))in a manner that would be well-understood, routine, and conventional.
Dependent claims 2-9 and 11-18 do not include any additional elements beyond those already recited in independent claims 1 and 10. Therefore, they are not deemed to be significantly more than the abstract idea because, as stated above, the limitations of the aforementioned dependent claims amount to no more than generally linking the abstract idea to a particular technological environment or field of use, and/or do not recite and additional elements not already recited in independent claims 1 and 10, hence do not amount to “significantly more” than the abstract idea.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-5, 8-9, 10-14, and 17-18 are rejected under 35 U.S.C. 103 is being unpatentable over Ury(US10586612B2) in view of Emanuel(US20170103163A1) and Zimmerman(US20190005200A1).
Claim 1
Ury discloses:
A system for collecting, displaying, and modeling a patient medical record, comprising: a processor; a main memory in communication with the processor via a communication infrastructure, said memory including stored instructions that, when executed by said processor, cause said processor to: access an electronic health record(Col. 18, Line 56, Ury discloses: “electronic-health-record (“EHR”)”) including clinical data corresponding to a patient(Col. 24, Line 26, Ury discloses: “medical information relevant to the particular patient”[MEDICAL INFORMATION CAN BE CLINICAL DATA CORRESPONDING TO A PATIENT]), the clinical data normalized to a Fast Healthcare Interoperability Resources (FHIR) format(Para 0045, Emanuel discloses FHIR); analyze the clinical data to create a problem list(Col. 20, Line 61, Ury discloses: “symptoms” [SYMPTOMS CAN BE A PROBLEM LIST]) including one or more medical diagnoses(Col. 20, Line 61, Ury discloses: “diagnoses”) associated with the patient(Col. 24, Line 39, Ury discloses: “directed to identifying all possible clinical actions that might be relevant to a particular patient, in which case patient data is used to select all possible candidate subtrees and to then evaluate the relevance…”[EVALUATING PATIENT DATA FOR POTENTIAL CLINICAL ACTIONS CAN BE SIMILAR TO ANALYZING PATIENT DATA FOR POTENTIAL PROBLEMS TO BE ADDRESSED]); retrieve, via one or more FHIR(Para 0045, Emanuel discloses FHIR) genomic operations(Col. 23, Line 52, Ury discloses a query producing information about genetic variants, which can be a genomic operation), genomic data corresponding to the patient(Col. 17, Line 42, Ury discloses: “genetic data for individual patients…”), wherein said genomic data is stored in a genomic server(Col.2, Line 29, Ury discloses: “Individual patient data and clinical-knowledge databases, including the network-like clinical-knowledge data structures, are hosted in cloud-computing-like data centers…”[DATA CENTERS CAN ACT AS A STORAGE SERVE FOR GENOMIC DATA]), said genomic server configured to interface with the electronic health record, wherein executing the one or more FHIR genomic operations comprises performing server-side normalization of variant data and genomic liftover across heterogeneous reference assemblies(Para 0045, Emanuel discloses FHIR, which inherently comprises server-side normalization); generate a digital twin(Para 0031, Zimmerman discloses: “digital twin”) based on the problem list, the clinical data, and the genomic data; output said digital twin(Para 0058, Zimmerman discloses: “Execution of the algorithms via the intelligent care ecosystem 1030 using the digital twin 130 creates output(s) that can be synthesized to be provided to the digital twin 130 and/or other system, for example. In certain examples, an action plan (e.g., a patient care plan, etc.) can be created from the synthesized output.”) to a user, wherein said digital twin includes interactive components corresponding to at least one of a genome, clinical condition, treatment(Para 0038, Zimmerman discloses: “healthcare practitioner can view and simulate[INTERACT] with the digital twin 130 to evaluate a condition[CLINICAL CONDITION], progression, possible treatment[TREATMENT], etc., for the patient.”), and clinical trial; receive, from the user, a user query via the interactive components query(Figure 19, Ury discloses a user query process), using one or more FHIR(Para 0045, Emanuel discloses FHIR) phenotype operations(Col. 23, Line 52, Ury discloses a query producing information about expressed proteins, which can be a phenotype operation), the genomic data and the clinical data based on the user query(Col. 23, Line 52, Ury discloses a query producing information about genomic variants and clinical data): and receive at least one of a diagnostic implication(Col. 26, Line 27, Ury discloses diagnosis-related clinical-action node) and therapeutic implication for the patient as output from the one or more FHIR(Para 0045, Emanuel discloses FHIR)phenotype operations.
Ury does not explicitly disclose:
FHIR
digital twin
output
digital twin
clinical condition
treatment
Emanuel discloses:
FHIR
Before the effective filing date of the claimed invention, it would have been obvious to one of
ordinary skill in the art to have modified the cloud-like medical-information service of Ury to add FHIR, as taught by Emanuel. One of ordinary skill would have been so motivated to provide a means to apply a specific format for data to be presented, but in this case for a method/system for a cloud-enabled health record exchange engine(Para 0002, Emanuel discloses: “To reduce the cost of interoperability, software components and methodologies must be produced that reduce the high cost of healthcare interoperability for systems that are sharing healthcare information using a diversity of “information formats” standards outlined by the Meaningful Use regulation.”)
Emanuel does not explicitly disclose:
digital twin
output
digital twin
clinical condition
treatment
Zimmerman discloses: digital twin, clinical condition, treatment
digital twin(Para 0031, Zimmerman discloses: “digital twin”)
output said digital twin(Para 0058, Zimmerman discloses: “Execution of the algorithms via the intelligent care ecosystem 1030 using the digital twin 130 creates output(s) that can be synthesized to be provided to the digital twin 130 and/or other system, for example. In certain examples, an action plan (e.g., a patient care plan, etc.) can be created from the synthesized output.”)
clinical condition, treatment(Para 0038, Zimmerman discloses: “healthcare practitioner can view and simulate[INTERACT] with the digital twin 130 to evaluate a condition[CLINICAL CONDITION], progression, possible treatment[TREATMENT], etc., for the patient.”)
Before the effective filing date of the claimed invention, it would have been obvious to one of
ordinary skill in the art to have modified the cloud-like medical-information service of Ury to add digital twin, output digital twin, clinical condition, and treatment, as taught by Zimmerman. One of ordinary skill would have been so motivated to provide a means to create a digital twin of a patient based on genomic data and medical records and output potential clinical conditions and potential treatment post-analysis of the data, but in this case for a method/system for generating a patient (Para 0003, Zimmerman discloses: “Healthcare provider consolidations create geographically distributed hospital networks in which physical contact with systems is too costly. At the same time, referring physicians want more direct access to supporting data in reports and other data forms along with better channels for collaboration. Physicians have more patients, less time, and are inundated with huge amounts of data, and they are eager for assistance.”)
Claim 2
Ury discloses:
The system of claim 1, wherein said processor is further operative to retrieve phenotype information(Col. 20, Line 62, Ury discloses: “phenotype”) corresponding to said clinical data corresponding to the patient(Col. 24, Line 26, Ury discloses: “medical information relevant to the particular patient”[MEDICAL INFORMATION CAN BE CLINICAL DATA CORRESPONDING TO A PATIENT]).
Claim 3
Ury discloses:
The system of claim 1, wherein said one or more FHIR genomic operations facilitate determining simple or structural variants(Figure 20, Ury discloses genomic variants present in genomic data) are present in said genomic data(Col. 17, Line 42, Ury discloses: “genetic data for individual patients…”).
Claim 4
Ury discloses:
The system of claim 1, wherein said one or more FHIR genomic operations facilitate retrieving haplotypes(Col. 17, Line 52, Ury discloses: “”single nucleotide polymporphism” or “SNP” [SNPs ARE HAPLOTYPES]) or genotypes(Col. 18, Line 13, Ury discloses: “chromosome” [CHROMOSOME CAN INDICATE GENOTYPE]) for one or more specified genes.
Claim 5
Ury discloses:
The system of claim 1, wherein said one or more FHIR genomic operations facilitate retrieving diagnostic implications for one or more variants(Col. 19, Line 48, Ury discloses: “EHR application may request the cloud-like medical-information service to compare the patient's gene variants with the clinical knowledge maintained by the cloud-like medical-information service in order to find any genomic indications that would support or argue against the diagnosis or planned therapy.”).
Claim 8
Ury discloses:
The system of claim 1, wherein each interactive components is output as one or more data clusters, each data cluster linked to said health record(Figure 21, Ury discloses data clusters that can be linked to a health record) and formed by a plurality of nodes(Figure 16A, #1610, #1612, Ury discloses a plurality of nodes).
Claim 9
Ury discloses:
The system of claim 1, wherein said plurality of nodes extends from a central node(Col. 25, Line 14, Ury discloses: “root node” [ROOT NODE CAN BE A CENTRAL NODE]), said central node associated with an identified region of interest and at least one of said clinical data and genomic data(Figure 16A, #1622, #1612, Ury discloses a clinical and genomic data nodes).
Claim 10
Claim 10 recites similar limitation as claim 1. See claim 1 analysis.
Claim 11
Claim 11 recites similar limitation as claim 2. See claim 2 analysis.
Claim 12
Claim 12 recites similar limitation as claim 3. See claim 3 analysis.
Claim 13
Claim 13 recites similar limitation as claim 4. See claim 4 analysis.
Claim 14
Claim 14 recites similar limitation as claim 5. See claim 5 analysis.
Claim 17
Claim 17 recites similar limitation as claim 8. See claim 8 analysis.
Claim 18
Claim 18 recites similar limitation as claim 9. See claim 9 analysis.
Claims 6-7 and 16-17 are rejected under 35 U.S.C. 103 is being unpatentable over Ury(US10586612B2) in view of Emanuel(US20170103163A1) and Zimmerman(US20190005200A1), and in further view of Srinivasa(US20230315738A1)
Claim 6
Ury, Emanuel, and Zimmerman do not explicitly disclose:
The system of claim 1, wherein said one or more FHIR genomic operations facilitate retrieving a list of patients corresponding to at least one of specified variants, structural intersecting variants, structural subsuming variants, and specified genotypes or haplotypes.
Srinivasa discloses:
The system of claim 1, wherein said one or more genomic operations facilitate retrieving a list of patients corresponding to at least one of specified variants, structural intersecting variants, structural subsuming variants, and specified genotypes or haplotypes(Para 0163, Srinivasa discloses: “The initial list of patients may be used to extract a first narrowed list of patients and associated KRAS mutation information[MUTATION CAN BE CONSIDERED A VARIANT] from the omics data store 1706.[OMICS DATA CAN INCLUDE VARIANT, GENOTYPE, AND HAPLOTYPE DATA]”).
Before the effective filing date of the claimed invention, it would have been obvious to one of
ordinary skill in the art to have modified that cloud-like medical-information service of Ury to add a list of patients corresponding to at least one of specified variants, structural intersecting variants, structural subsuming variants, and specified genotypes or haplotypes, as taught by Srinivasa. One of ordinary skill would have been so motivated to provide a means to access individuals which certain genetic traits for potential identification of clinical trial or research study candidates, but in this case for a method/system for integrating data for precision medicine(Para 0010, Srinivasa discloses: “Thus, realization of the potential promise of precision medicine relies on accessing and analyzing large, multi-dimensional datasets. The isolation of biomedical data in separate silos makes this challenging.”
Claim 7
Ury discloses:
The system of claim 1, wherein said one or more FHIR operations facilitate retrieving metadata(Para 0055, Srinivasa discloses: “metadata”) associated with one or more sequencing studies performed on a subject(Col. 17, Line 43, Ury discloses: “Genetic data for individual patients can then be stored as a list of variations, or variants, with respect to the reference sequence. “).
Ury, Emanuel, and Zimmerman do not explicitly disclose: metadata
Srinivasa discloses: metadata
metadata(Para 0055, Srinivasa discloses: “metadata”)
Before the effective filing date of the claimed invention, it would have been obvious to one of
ordinary skill in the art to have modified the cloud-like medical-information service of Ury to add metadata, as taught by Srinivasa. One of ordinary skill would have been so motivated to provide a means to analyze and process data with its lineage being traceable, but in this case for a method/system for integrating data for precision medicine(Para 0010, Srinivasa discloses: “Thus, realization of the potential promise of precision medicine relies on accessing and analyzing large, multi-dimensional datasets. The isolation of biomedical data in separate silos makes this challenging.”
Claim 15
Claim 15 recites similar limitation as claim 6. See claim 6 analysis.
Claim 16
Claim 16 recites similar limitation as claim 7. See claim 7 analysis.
Response to Arguments
35 U.S.C. 101
(Page 8) Regarding the assertion that the amendments to claims 1 and 10 render the claims such that they cannot be performed in the human mind.
Applicant's arguments filed have been fully considered but they are not persuasive. Please refer to updated 101 analysis above for amended claims.
(Pages 8-10) Regarding the assertion that the claims are directed toward a practical application because they integrate the alleged judicial exception into a practical application.
Applicant's arguments filed have been fully considered but they are not persuasive. Please refer to updated 101 analysis above for amended claims.
(Pages 10-11) Regarding the assertion that the claims recite significantly more than the abstract idea.
Applicant's arguments filed have been fully considered but they are not persuasive. Please refer to updated 101 analysis above for amended claims.
35 U.S.C. 103
(Pages 12-13) Regarding the assertion that Ury, Zimmerman, and Srinivasa do not teach FHIR.
Applicant’s arguments have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Emanuel(US20170103163A1).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Mansi(US20210151187A1): Mansi discloses data-driven estimation of predictive digital twin models from medical data. Some disclosures of this invention are similar to that of this instant pending application. (Specifications, para 0069 and 0079)
Davies(US7529685B2): Davies discloses system for storing, retrieving, and integrating clinical, diagnostic, genomic, and therapeutic data. Some disclosures of this invention are similar to that of this instant pending application. (Specifications, para 0048 to 0065)
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/S.G.P./Examiner, Art Unit 3685
/KAMBIZ ABDI/Supervisory Patent Examiner, Art Unit 3685