DETAILED ACTION
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 .
Applicant's amendments and remarks, filed 12/05/2025, are acknowledged. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Status of Claims
Claims 1-24 are presently under examination. Claim 24 is newly added.
Priority
This application claims priority to U.S. Provisional Application No. 63/078,215, filed September 14, 2020.
Withdrawn Rejections
The rejection of claims 1-23 under 35 U.S.C. 101 because the claimed invention is not supported by either a substantial asserted utility or a well-established utility is withdrawn in view of applicant’s amendments.
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.
This rejection is modified in view of applicant’s amendments.
Claims 1-24 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.
The United States Patent and Trademark Office published revised guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”). Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes) (Guidance Step 2A, Prong 1); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and conventional in the field” (see MPEP § 2106.05(d)); or 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019).
(4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
Step 1
The instantly claimed invention (claim 1 being representative) requires performing a series of process steps. As such, the claims fall into one of the four statutory categories.
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. Regarding claim(s) 1, the following limitations constitute the abstract idea for the following reasons:
creating and structuring a custom file according to the data structure defined by the schema stored in the memory by:
obtaining, by one or more processors, according to the schema, a plurality of nucleic acid sequencing analysis files, wherein each one of the plurality of nucleic acid sequencing analysis files comprises nucleic acid sequence information, genetic variant information, gene expression information, or any combination thereof, of a plurality of biological samples, wherein the plurality of biological samples comprise the desired sample; for each one of the plurality of nucleic acid sequencing analysis files: determining, according to the schema, a plurality of data objects in the nucleic acid sequencing analysis file to be stored in the custom file;
determining, according to the schema, a plurality of custom data fields in the custom file to store the data objects;
generating a checksum by evaluating a cryptographic hash function for a portion of the custom file according to the schema;
Mental Processes
Under the BRI, the above steps are not limited to any particular acts or operations to achieve the claimed functions and amount to observation, collection, and manipulation of data. Information is intangible, and data analysis and algorithms are abstract ideas. See, e.g., Microsoft Corp. v. AT&T Corp., 550 U.S. 437, 451 n.12 (2007); Alice, 134 S. Ct. at 2355; Parker v. Flook, 437 U.S. 584, 594- 95 (1978). Similarly, information collection and analysis, including when limited to particular content, is within the realm of abstract ideas. See, e.g., Internet Patents Corp. v. Active Network, Inc., 790 F.3d 1343, 1349 (Fed. Cir. 2015); Digitech Image Techs., LLC v. Elecs.for Imaging, Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014); CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1370 (Fed. Cir. 2011). That is, "[w]ithout additional limitations, a process that employs mathematical algorithms to manipulate existing information to generate additional information is not patent eligible." Digitech, 758 F.3d at 1349-51 ("Data in its ethereal, non-physical form is simply information that does not fall under any of the categories of eligible subject matter under section 101. "). In addition, the specification also provides sufficient evidence that the claims are directed to an abstract idea by accomplishing these tasks include only computational analysis and/or mathematical functions [0009, 0016-0019]. For these reasons, the above steps fall within the “mental processes” grouping of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III [Step 2A, Prong 1: YES].
Mathematical Concept
With regards to the generating step, this requires generating a checksum using a hash function. The specification also teaches that specific hash functions to achieve this result [0016-0019]. Accordingly, this step can be broadly interpreted as encompassing mathematical calculations, i.e. similarly to the claims in Gottschalk v. Benson, 409 U.S. 63, 67 (1972). Therefore, when read in light of applicant’s own specification, the claims are directed to a mathematical concept. See MPEP 2106.04 and 2106.05(II). [Step 2A, Prong 1: YES].
Organizing Data
Under the BRI, the above steps recite a method of organizing human activity. The claimed invention is a method that allows a user to receive a query for information, organizing information (i.e. schema); obtaining a plurality of DNA sequence files; determining data objects and custom fields in said files, storing data objects in said files, generating a mathematical number (i.e. checksum) using hash functions for a portion of the files, and storing the checksum. Therefore, absent any particular acts or operations to achieve the claimed functions and absent any suitably programmed computer processor/hardware, the claimed method broadly encompasses managing and organizing data, e.g., a computer programmer merely inputting data into a spreadsheet and assigning numerical values to said data. Thus, the claim recites an abstract idea.
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim includes any additional steps/elements that integrate the recited judicial exception into a practical application of the exception. In this case, the additional steps/elements that are not part of the abstract idea are as follows:
receiving a query for information associated with a desired sample;
determining an electronic schema chosen from a plurality of pre-defined electronic schemas stored in a memory, wherein the schema defines a data structure for a custom file to be created for the desired sample;
storing the data objects in the custom data fields; storing the checksum in the custom file.
In this case, the receiving step is not limited to any particular techniques or devices and results in obtaining data for use by the abstract idea. Therefore, this step amounts to insignificant extra-solution activity and is not indicative of an integration into a practical application. See MPEP 2106.05(g). With regards to the storing steps, these amount to nothing more than insignificant extra-solution activity and are not indicative of an integration into a practical application. See MPEP 2106.05(g).
With regards to the determining step (wherein a ‘schema defines a data structure’), the schema is recited at a high of generality (without any details regarding structure). Accordingly, this step amounts to “selecting” a generically recited data structure that is used as a tool to perform the abstract idea and/or merely indicate instructions to implement the abstract idea on a computer. Therefore, this step amounts to nothing more than “insignificant extra-solution activity” and/or an attempt to generally link the use of the judicial exception to the technological environment of a computer. See MPEP 2106.05(g). See MPEP 2106.05(h).
With regards to the generically recited processors, it is well established that “generic computer components such as a computer and database do not satisfy the inventive concept requirement.” See MPEP 2106.05(h). Even when viewed in combination, these additional steps/elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO]
For a list of considerations when evaluating whether additional elements integrate a judicial exception into a practical application see MPEP 2106.04(d)(1) lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using 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, as discussed in MPEP § 2106.05(e).
C. Guidance Step 2B:
Under the 2019 PEG, a conclusion that an additional element is insignificant extra-solution activity in Step 2A should be re-evaluated in Step 2B. In this case, the claims do not include additional steps and/or elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons:
As discussed above, the non-abstract steps (including the full limitations and not just the verbs) amount to nothing more than insignificant extra-solution activity. A review of the specification teaches routine and conventional computer hardware and software for performing these steps [0074]. In addition, Maltbie et al. (WO2013049420A1) teaches a system and method for facilitating network-based transactions involving routine and conventional codec schema [Figure 5] as well as methods for receiving queries [1041-43, 1047] and storing checksums in files [1149, 1152, 1231]. Accordingly, there is nothing unconventional with regards to the claimed assays for obtaining expression data. In addition, to the extent that applicant intends for the claimed analysis to be performed by a computer, the courts have also explained that the use of generic computer elements do not alone transform an otherwise abstract idea into patent-eligible subject matter. See DDR Holdings (Fed. Cir. 2014). Even when considered in combination, these additional steps/elements do not provide an inventive concept [Step 2B: NO].
Dependent Claims
Dependent claims 2-24 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. Regarding claim(s) 2-20, these claims further limit the specificity of the abstract idea set forth above, and/or the specificity of the data being used by the abstract idea (i.e. data is abstract). Accordingly, these steps also encompass an abstract idea for the reasons set forth above [Step 2A, prong 1]. Regarding claim(s) 21, 22, 23,24, these claims are directed to a database, system, and computer program product for performing the method of claim 1. However, these claims are also not patent eligible for reasons set forth above. Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more.
Response to Arguments
Applicant’s arguments, filed 12/05/2025, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the claimed method, as amended, provides an improvement to computer functionality. In response, the claims are directed to creating and structuring a custom file (i.e. an abstract idea) that is implemented (according to a generic scheme) on a generic computer processor recited at a high level of generality. As such, there is nothing in the specification to support applicant’s position that the claimed invention is directed to an improvement in a particular machine, computer, or computer functionality (as in Enfish). Unlike the McRO decision, where the ultimate product produced was a synchronized computer animation that was itself the transformative use, the result of the presently claimed method is information itself, without being directed to any particular use of that information. See also Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1355 (Fed. Cir. 2016) (“[Merely selecting information, by content or source, for collection, analysis, and display does nothing significant to differentiate a process from ordinary mental processes.”). As such, the examiner maintains that the claims do not integrate the recited judicial exception into a practical application.
In addition, neither applicant nor the specification provides any objective evidence showing how the claimed invention improves the functioning of a computer. At best, the specification teaches a need for “improved techniques in the management of such information before, during, and after the genomic analysis workflow” [0007]. However, this is not recited in the claims and does not show how the claimed invention improves the functioning of a computer. To the extent that the creating and structural step is the inventive concept, applicant is reminded that the claimed invention’s use of the ineligible concept to which it is directed (i.e. the abstract idea) cannot supply the inventive concept that renders the invention ‘significantly more’ than that ineligible concept.” BSG Tech LLC v. BuySeasons, Inc., 899 F.3d 1281, 1290 (Fed. Cir. 2018). It is also well settled that mere computer-based efficiency does not save an otherwise abstract method. Bancorp Servs. L.L.C. v. Sun Life Assur. Co. of Canada (US.), 687 F.3d 1266, 1277-78 (Fed. Cir. 2012) (explaining that performance by computer of operations that previously were performed manually or mentally, albeit less efficiently, does not convert a known abstract idea into eligible subject matter). As such, the claimed invention does not provide an improvement to computer functionality. For at least these reasons, and absent any evidence to the contrary, the rejection is maintained.
Claim rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(a):
IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same and shall set forth the best mode contemplated by the inventor of carrying out his invention.
This new matter rejection is necessitated by applicant’s amendments.
Claims 1-24 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 recites “determining an electronic schema chosen from a plurality of pre-defined electronic schemas stored in a memory, wherein the schema defines a data structure for a custom file to be created for the desired sample.” While there is no in haec verba requirement, newly added claims or claim limitations must be supported in the specification through express, implicit, or inherent disclosure. In this case, however, the examiner cannot find support for “wherein the schema defines a data structure for a custom file to be created for the desired sample” in the original claims, drawings, or the specification as originally filed, and no basis has been pointed to for these new limitations in applicant's remarks. In the absence of support for the newly recited limitations, these claims and claims dependent thereon are deemed to constitute new matter.
Claim rejections - 35 USC § 112 - Indefiniteness
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.
This rejection is modified in view of applicant’s amendments.
Claims 1-24 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 pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 1 is/are also rejected due to said dependency.
Claim 1 recites “receiving a query…associated with a desired sample”. In this case, it is unclear as to who (or what) is actually “receiving” (and performing) the query. Notably, the claims do not presently recite any “user” or any hardware for performing this function as claimed. Clarification is again requested via amendment.
Claim 1 recites “determining an electronic schema chosen from a plurality of pre-defined electronic schemas stored in a memory, wherein the schema defines a data structure for a custom file to be created for the desired sample.” This phrase is problematic for the following reasons. (1) It is unclear as to the metes and bounds of the term “schema”, which ambiguously encompasses physical schema, logical schema, operational schema, codec schema, and otherwise. A review of the specification does not provide any limiting definition that would serve to clarify the scope such that the artisan would recognize what structural and/or functional limitation is intended. (2) As a result, it is also unclear what functional limitation is intended by the ‘determining’ step, which amounts to generic functional claim language and descriptions of problems to be solved. A review of the specification does not describe any algorithms, equations, or prose equivalent that correspond to the claimed function. (3) It is unclear what limiting effect is intended by the above “wherein” clause, i.e. in what way does the claimed schema “define a data structure”. A review of the specification does not provide any limiting definition that would serve to clarify what structural limitation is intended. Clarification is requested via amendment, as Applicant has not provided any illuminating arguments or clarifying amendments that would serve to overcome this issue.
Claims 1, 3, 4, 8, 13, 14, 15 all recite “according to the schema”. In light of the issues set forth above regarding the term “schema”, it remains unclear what limiting effect is intended by the phrase “according to the scheme”. Stated differently, it is unclear in what way the positive process limitations recited in the instantly rejected claims are performed “according to the schema”. A review of the specification does not provide any limiting definition that would serve to clarify the scope. In each case, clarification is again requested via amendment, as Applicant has not provided any illuminating arguments or clarifying amendments that would serve to overcome this issue.
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).
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103(a) 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.
This rejection is modified in view of applicant’s amendments.
Claims 1, 3, 5-11, 16-24 are rejected under 35 U.S.C. 103(a) as being unpatentable over Maltbie et al. (WO2013/049420).
Regarding claim(s) 1, Maltbie teaches systems and methods for facilitating uploading, downloading and other network-based transactions involving sequence information, such as large files of genomic sequence data are described.
In particular, Maltbie teaches functionality for receiving a query to verify that submitted data is associated with a valid sample [para. 1043, and ref. claims 1-9], including functionality to retrieve catalog information from an external source and allow users to perform queries across project, sample, and sequence data [para. 1043, and ref. claims 1-9], which reads on receiving as claimed.
Maltbie teaches determining a codec schema representative of various encoding, decoding, encryption, decryption and transcoding operations which may be effected within the data network [01057-0162], which broadly reads on determining an electronic schema that defines a data structure as claimed. In this case, the various types of encryption and decryption functions are reasonably interpreted as pre-defined electronic schemas absent any limiting definition to the contrary.
Maltbie teaches functionality for receiving, from over a network, a plurality of portions of at least one file of biological sequence data conveyed over the network in accordance with a parallel file transfer process wherein ones of the plurality of portions are transferred substantially simultaneously in multiple data streams and stored [1014-1015 and Figures 4 and 5], which reads on said obtaining.
Maltbie teaches functionality for determining and storing a plurality of data units containing the encoded genomic information and the biological information [01016 and Figures 4 and 5], which reads on determining and storing as claimed.
Maltbie teaches decoding files and generating a reconstructed file (i.e. custom file) of biological sequence data by reconstructing the at least one file of biological sequence data using the plurality of portions of the at least one file of biological sequence data [1014-1016, Figure 4, and Figure 5, ref. claims 1-9].
Maltbie does not specifically teach generating a checksum by evaluating a cryptographic hash function for a portion of the custom file, as claimed. However, Maltbie at a minimum suggests this feature by performing a series of validation steps prior to making the data available for download, including computing the MD5 checksum and comparing it against the value in the XML metadata file [1149] and since one of ordinary skill in the art would recognize that the MD5 checksum including a 128-bit cryptographic hash function.
Regarding claim(s) 3, Maltbie teaches functionality for searching the database for specify values for one or more metadata attribute fields within the query [1151] and copying data [1169].
Regarding claim(s) 5, 6, 7, 8, 9, Maltbie teaches using data associated with a whole genome or whole exome sequence data, as well as annotation data concerning functional regions of the genome, genes, promoters, repeat sequences, DNA methylations, SNPs, CNVs, structural variants including chromosomal rearrangements [1241]; case/sample ID numbers [1253]; and data units containing the encoded genomic information and the biological information [01016 and Figures 4 and 5], as set forth above.
Regarding claim(s) 10, 11, Maltbie using the MD5 checksum, comparing it against the value in the XML metadata file, and storing the result [1149, Figure 5].
Regarding claim(s) 16, 17, 18, 19, Maltbie teaches functionality encoding, decoding, and compression of the sequence entries [1121; 1014-1016, Figure 4, and Figure 5]; and using XML formats [1141].
Regarding claim(s) 20, 21, 22, 23, 24, Maltbie teaches using computer processors and network of servers communicating over one or more existing wide area networks, such as the Internet (i.e. cloud computing) and parallel processing [1039-1040, and Figures 4, 5, 12], as claimed.
Conclusion
No claims are 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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619