DETAILED ACTION
Applicant’s response filed 10/07/2025 has been fully considered. The following rejections and/or objections are either reiterated or newly applied.
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 .
Claim Status
Claims 2-3, 11 and 17 are cancelled by Applicant.
Claim 21 is newly added by Applicant.
Claims 1, 4-10, 12-16 and 18-21 are currently pending and are herein under examination.
Claims 1, 4-10, 12-16 and 18-21 are rejected.
Claim 21 is objected.
Priority
The instant application does not claim benefit of priority to any earlier filed applications. Therefore, the effective filing date for instant claims 1, 4-10, 12-16 and 18-21 is 03/10/2021.
Withdrawn Rejections
35 USC 103
The rejection of claims 1-2, 4, 10 and 16 under 35 U.S.C. 103 as being unpatentable over Tijanic et al. in view of Jian et al. and Deelman et al. is withdrawn in view of Applicant’s claim amendments. Applicant has incorporated claim 3, which was free from the prior art, into independent claims 1, 10 and 16.
The rejection of claims 6-7, 13 and 19 under 35 U.S.C. 103 as being unpatentable over Tijanic et al. in view of Jian et al. and Deelman et al. and in further view of Cieslik et al. and Reichert et al. is withdrawn in view of Applicant’s claim amendments. Applicant has incorporated claim 3, which was free from the prior art, into independent claims 1, 10 and 16.
The rejection of claims 8, 14 and 20 under 35 U.S.C. 103 as being unpatentable over Tijanic et al. in view of Jian et al. and Deelman et al. and in further view of Kintsakis et al. is withdrawn in view of Applicant’s claim amendments. Applicant has incorporated claim 3, which was free from the prior art, into independent claims 1, 10 and 16.
The rejection of claims 9 and 15 under 35 U.S.C. 103 as being unpatentable over Tijanic et al. in view of Jian et al. and Deelman et al. and in further view of Ejigu et al. is withdrawn in view of Applicant’s claim amendments. Applicant has incorporated claim 3, which was free from the prior art, into independent claims 1, 10 and 16.
Claim Interpretation
The computer program product in claim 10 is being interpreted as non-transitory because specification para. [17] states that a computer-readable storage medium is not to be construed as transitory signals. As such, claim 10 was not rejected under 35 USC 101 for not being directed to a category of statutory subject matter.
Claim Objection
The objection to claim 12 is withdrawn in view of Applicant’s amendments. It is noted that in the previous Office action examiner mistakenly wrote claim 14. However, it was meant to be claim 12. Applicant identified the error.
Claim 21 is objected to because of the following informalities:
Claim 21, recites the phrase “The method of claim 1” which should be “The computer-implemented method of claim 1”.
Claim 21 recites the phrase “the second bioinformatics processing to” which should be “the second bioinformatics processing tool to”.
Claim 21 recites the phrase “dataset set” which should be “dataset”.
Claim 21, line 2, should have the verb “is” before the phrase “in parallel” to correct the grammar of the clause.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
35 USC 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(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 the first paragraph of pre-AIA 35 U.S.C. 112:
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.
Claim 21 is 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. This rejection is newly recited and necessitated by claim amendment.
Claim 21 recites new matter. Claim 21 requires the third tool to process the first portion of the dataset in parallel with the second tool processing the second portion of the dataset, wherein the second portion is a remaining portion of the dataset. Claim 1 requires a processing order of 1st tool > 3rd tool > 2nd tool. The disclosure discusses parallel processing as in claim 21 and the processing order of 1st tool > 3rd tool > 2nd tool as in claim 1 as separate embodiments. However, there does not appear to be disclosure for performing the processing order of 1st tool > 3rd tool > 2nd at the same time as the parallel processing in claim 21.
35 USC 112(b)
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 5-7, 12-13, 18-19 and 21 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. This rejection is newly recited and necessitated by claim amendment.
Claims 5, 12 and 18 recite the phrase “instructing the second bioinformatics processing tool to process the bioinformatics dataset” which renders the claims indefinite. Claims 1, 10 and 16 require that the third tool replace the second tool for at least the first portion of the dataset. However, claims 5, 12 and 18 require that the second tool process the entire dataset, which includes the first portion. Thus, it is unclear if the second tool processes only the remaining portion of the dataset, or if the second tool processes the entire dataset. To overcome this rejection, it is suggested to clarify what the second tool processes. For examination purposes, claims 5, 12 and 18 are being interpreted to mean that the second tool processes the remaining portion of the dataset rather than the entire dataset.
Claims 6, 13 and 19 are indefinite because they recite that the determined modification is an added branch that requires the second and third tool to process in parallel the first portion of the dataset. However, claims 1, 10 and 16 recite that the determined modification requires the third tool to replace the second tool for at least the first portion, wherein the second tool processes a remaining portion. Thus, it is unclear which portions of the dataset are processed by which tools. To overcome this rejection, it is suggested to clarify the sequence of processing events and clarify which tools process which data. For examination purposes, claims 6, 13 and 19 are being interpreted to replace the determined modification in claims 1, 10 and 16, respectively. This interpretation necessitates a rejection of claims 6, 13 and 19 under 35 USC 112(d). See the rejection below.
Furthermore, claim 7 is also rejected because it includes the limitations of claim 6, which is rejected, and because it does not resolve the issue of indefiniteness.
Claims 7, 13 and 19 recite the phrase “instructing the second bioinformatics processing tool to process the bioinformatics dataset” which renders these claims indefinite. Claims 1, 10 and 16 require that the second tool processes a second remaining portion of the dataset. However, claims 7, 13 and 19 require that the second tool process the entire dataset, which includes the first portion. Thus, it is unclear if the second tool processes only the second remaining portion of the dataset, or if the second tool processes the entire dataset. To overcome this rejection, it is suggested to clarify what the second tool processes. For examination purposes, claims 7, 13 and 19 are being interpreted to mean that the second tool processes the remaining portion of the dataset rather than the entire dataset.
Claim 21 is indefinite because it requires that the third tool process the first portion in parallel with the second tool that processes the second portion. However, claim 1 requires a non-parallel processing order of 1st tool -> 3rd tool -> 2nd tool. Thus, the order of processing events is unclear. To overcome this rejection, it is suggested to clarify the sequence of processing events. For examination purposes, claim 21 is being interpreted to replace the order in claim 1 of 1st tool -> 3rd tool -> 2nd tool with an order of 1st tool -> parallel processing using 2nd and 3rd tool. This interpretation necessitates a rejection under 35 USC 112(d). See the rejection below.
35 USC 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 4, 6, 13, 19 and 21 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. This rejection is newly recited and necessitated by claim amendment.
Claim 4 fails to further limit claim 1. Claim 4 requires the determined modification be for at least the first portion of the dataset. However, claim 1, lines 14-17, requires that the determined modification already be for at least the first portion of the dataset.
Claims 6, 13 and 19 fail to include all the limitations of claims 1, 10 and 16, respectively. Claims 6, 13 and 19 require that the second and third tool process in parallel the first portion of the dataset. However, claims 1, 10 and 16 require that the third tool replace the second tool for processing at least the first portion of the dataset.
Claim 21 fails to include all the limitations of claim 1. Claim 21 requires that the third tool process the first portion in parallel with the second tool that processes the second portion. However, claim 1 requires a non-parallel processing order of 1st tool -> 3rd tool -> 2nd tool.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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, 4-10, 12-16 and 18-21 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Any newly recited portions herein are necessitated by claim amendment.
Step 2A, Prong 1:
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: Yes) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomena (Step 2A, Prong 1). In the instant application, claims 1, 4-9 and 21 recite a method, claims 10 and 12-15 recite a computer program product, and claims 16 and 18-20 recite a computer system. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claims 1, 10 and 16 recite “identifying a bioinformatics dataset and instructions for processing the bioinformatics dataset, the instructions identifying a sequence of bioinformatics processing tools including at least a first bioinformatics processing tool followed by a second bioinformatics processing tool, wherein the sequence does not initially include a third bioinformatics processing tool; instructing the first bioinformatics processing tool to process the bioinformatics dataset in accordance with the instructions; analyzing an output of the first bioinformatics processing tool, utilizing a machine learning based decision model, to determine a modification to the sequence of bioinformatics processing tools; modifying, based on an observation from the analyzing, the sequence to add the third bioinformatics processing tool to the sequence in between the first bioinformatics processing tool and the second bioinformatics processing tool in the sequence, wherein the modifying is configured to produce an increase in an accuracy of a result of the sequence, and modifying replaces the second bioinformatics processing tool in the sequence of bioinformatics processing tools with the third bioinformatics processing tool for at least a first portion of the bioinformatics dataset; and instructing the third bioinformatics processing tool to process at least the first portion of the bioinformatics dataset in accordance with the determined modification and the second bioinformatics processing tool to process a second portion of the bioinformatics dataset in accordance with the sequence of bioinformatics processing tools, wherein the second portion is a remaining portion of the bioinformatics dataset.”
Claims 4, 12 and 18 recite “wherein the determined modification is for at least the first portion of the bioinformatics dataset.”
Claims 5, 12 and 18 recite “upon completion of the processing of the at least first portion of the bioinformatics dataset by the third bioinformatics processing tool, instructing the second bioinformatics processing tool to process the bioinformatics dataset.”
Claims 6, 13 and 19 recite “wherein the determined modification adds a branch to the sequence of bioinformatics processing tools, the branch instructing parallel processing of at least the first portion of the bioinformatics dataset by both the second bioinformatics processing tool and the third bioinformatics processing tool.”
Claims 7, 13 and 19 recite “instructing the second bioinformatics processing tool to process the bioinformatics dataset in parallel with the processing of the at least first portion of the bioinformatics dataset by the third bioinformatics processing tool.”
Claims 8, 14 and 20 recite “wherein the machine learning based decision model includes an artificial intelligence classifier, and wherein the method further comprises: training the artificial intelligence classifier utilizing historical bioinformatics datasets and a repository of bioinformatics processing tools, the repository of bioinformatics processing tools including at least one bioinformatics processing tool other than the bioinformatics processing tools included in the sequence of bioinformatics processing tools.”
Claims 9 and 15 recite “the bioinformatics dataset is a genomic dataset; and the first bioinformatics processing tool, the second bioinformatics processing tool, and the third bioinformatics processing tool are genomic annotation tools.”
Claim 21 recites ‘’wherein the second bioinformatics processing to process the second portion of the bioinformatics dataset set in parallel with the third bioinformatics processing tool processing the first portion of the bioinformatics dataset.”
Regarding the above cited limitations in claims 1, 4, 6, 8, 10, 12-14, 16 and 18-20 of identifying a bioinformatic dataset and instructions, analyzing an output of a bioinformatic tool, modifying the sequence by adding a third bioinformatic tool, and replacing/adding bioinformatic tools or branches in the sequence of bioinformatic tools, these limitations are recited at such a high level of generality that they can be practically performed in the human mind or by a human using pen and paper and therefore equate to a mental process. Specifically, a human can practically make identifications, analyze data, and modify the order of a sequence.
Regarding the above cited limitations in claims 8, 14 and 20 of using a machine learning model to determine modifications to the sequence of tools, and training an AI classifier on bioinformatic datasets and on different bioinformatic tools, these limitations are recited at such a high level of generality that a human could practically perform them by using pen and paper and therefore recite a mental process. Specifically, a human could perform the operations of a logistic regression (i.e., a classifier) to then use the output of the classifier to alter the parameters of the classifier. Furthermore, these limitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis, which the courts have established as limitations that can be practically performed in the human mind or by using pen and paper in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)).
Regarding claims 8, 14 and 20 of training an AI classifier on bioinformatic datasets and different bioinformatic tools, the broadest reasonable interpretation of training a classifier includes performing mathematical calculations to alter numerical parameters within the classifier, e.g., using a logistic regression. Therefore, these limitations equate to a mathematical concept. These limitations are also similar to organizing and manipulating information through mathematical correlations, which the courts have established as a mathematical concept in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)).
Regarding the above cited limitations in claims 1, 5-7, 10, 12-13, 16 and 18-19 of instructing bioinformatic tools to process or process in parallel, the broadest reasonable interpretation of these claims includes that they require following rules or instructions and therefore fall under the abstract ideas grouping of “Organizing Human Activity”, more specifically under managing personal behavior or relationships or interactions between people (See MPEP 210604(a)(2).II.C). The broadest reasonable interpretation of these claims includes, for example, them being instructions that a Principal Investigator might give to their research assistant to carry out.
Regarding the above cited limitations in claims 9, 15 and 21, these limitations are included in the recited judicial exception in claims 1 and 10 because they limit the bioinformatics dataset, the bioinformatic processing tools, and the instructions but do not change the fact that these limitations are part of the recited judicial exception.
As such, claims 1, 4-10, 12-16 and 18-21 recite an abstract idea (Step 2A, Prong 1: Yes).
Step 2A, Prong 2:
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to technology (MPEP § 2106.04(d)(1)) nor do they provide some other meaningful limitation. Rather, these claims merely include instructions to implement an abstract idea on a computer (MPEP § 2106.05(f)). The instant claims recite the following additional elements:
Claims 1 and 4-9 recite “a computer-implemented method”.
Claim 10 recites “A computer program product comprising one or more computer readable storage media and program instructions collectively stored on the one or more computer readable storage media, the program instructions executable by one or more processors to cause the one or more processors to perform a method comprising.”
Claims 12-15 recite “computer program product”.
Claim 16 recites “A computer system comprising: one or more processors; and one or more computer readable storage media; wherein: the one or more processors are structured, located, connected and/or programmed to execute program instructions collectively stored on the one or more computer readable storage media; and the program instructions, when executed by the one or more processors, cause the one or more processors to perform a method comprising.”
Claims 18-21 recite “The computer system of claim 16”
Regarding the above cited limitations in claims 1, 4-10, 12-16 and 18-21 of a computer program product, program instructions stored on a computer readable storage media, one or more processors, the computer-implemented method, and the computer system, nothing in the claims require that these limitations be anything other than a generic computing system. Therefore, these limitations equate to mere instructions to implement an abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp. 573 U.S. at 223, 110 USPQ2d at 1983.
As such, claims 1, 4-10, 12-16 and 18-21 are directed to an abstract idea (Step 2A, Prong 2: No).
Step 2B:
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions to apply the recited exception in a generic way or in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The instant claims recite the following additional elements:
Claims 1 and 4-9 recite “a computer-implemented method”.
Claim 10 recites “A computer program product comprising one or more computer readable storage media and program instructions collectively stored on the one or more computer readable storage media, the program instructions executable by one or more processors to cause the one or more processors to perform a method comprising.”
Claims 12-15 recite “computer program product”.
Claim 16 recites “A computer system comprising: one or more processors; and one or more computer readable storage media; wherein: the one or more processors are structured, located, connected and/or programmed to execute program instructions collectively stored on the one or more computer readable storage media; and the program instructions, when executed by the one or more processors, cause the one or more processors to perform a method comprising.”
Claims 18-21 recite “The computer system of claim 16”
Regarding the above cited limitations in claims 1, 4-10, 12-16 and 18-21 of a computer program product, program instructions stored on a computer readable storage media, one or more processors, the computer-implemented method, and the computer system, these limitations equate to instructions to implement an abstract idea on a generic computing system, which the courts have established does not provide an inventive concept in Intellectual Ventures I LLC v. Capital One Bank (USA), 792 F.3d 1363, 1367, 115 USPQ2d 1636, 1639 (Fed. Cir. 2015).
When these additional elements are considered individually and in combination, they all equate to instructions to implement an abstract idea on a generic computing system and to WURC components of a generic computing system, and therefore do not comprise an inventive concept that transforms the claimed judicial exception into a patent-eligible application of the judicial exception itself (Step 2B: No).
As such, claims 1, 4-10, 12-16 and 18-21 are not patent eligible.
Response to Arguments under 35 USC 101
Applicant's arguments filed 10/07/2025 have been fully considered but they are not persuasive.
Applicant argues that the following limitation in claims 1, 10 and 16 improves the technological field of bioinformatics processing and improves computer functionality by reducing the amount of computing resources needed to complete a task: “modifying, based on an observation from the analyzing, … wherein the modifying is configured to produce an increase in an accuracy of a result of the sequence” (pg. 11, para. 1 – pg. 12, para. 3 of Applicant’s remarks). Applicant’s argument is not persuasive for the following reasons:
It appears that the alleged improvement is a result of the judicial exception alone. MPEP 2106.05(a) recites “It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements.” The additional elements in claims 1, 10 and 16 are generic computers and generic computer components. However, these additional elements merely invoke a computer as a tool, which cannot provide a practical application under Step 2A, Prong 2 (MPEP 2106.05(f)(2)).
Furthermore, the abstract idea of “modifying, based on an observation from the analyzing, … wherein the modifying is configured to produce an increase in an accuracy of a result of the sequence, and modifying replaces the second bioinformatics processing tool in the sequence of bioinformatics processing tools with the third bioinformatics processing tool for at least a first portion of the bioinformatics dataset” merely presents a more efficient abstract idea, which necessarily requires less computational resources. However, using two bioinformatic tools to process different portions of a dataset does not actually alter the way that a general-purpose computer functions i.e., by changing the functioning of the processor itself or by changing the way in which it stores or accesses memory. Nothing about the physical components of the computer nor the way the computer operates is changed merely by providing the computer with a more efficient abstract idea. Therefore, it appears that the instant claims merely invoke computers as a tool (MPEP 2106.05(f)(2)). Moreover, see MPEP 2106.05(a)(I) regarding examples that do not improve computer functionality, specifically FairWarning IP, LLC v. Iatric Sys., 839 F.3d 1089, 1095, 120 USPQ2d 1293, 1296 (Fed. Cir. 2016).
Conclusion
No claims are allowed.
Claims 1, 4-10, 12-16 and 18-21 are free from the prior art because Applicant incorporated the limitations of claim 3 into independent claims 1, 10 and 16. Claim 3 was found to be free from the prior art in the Conclusion of the Office action mailed 12/131/2024.
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 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.
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/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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