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 .
Election/Restriction
Applicants’ election without traverse of Group II drawn to claims 7-13, filed 03/19/2026, is acknowledged. Applicant has failed to properly elect a species, as set forth in the restriction mailed 02/18/2026. However, after further consideration, the species requirement is hereby withdrawn as it is directed to non-elected claims. Claims 1-6 and 14-24 are hereby withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Status of Claims
Claims 7-13 are under examination.
Claims 1-6 and 14-24 are withdrawn.
Priority
Applicant’s claim for the benefit of priority under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. This application claims priority from Provisional Application No. 62/931,778, filed November 6, 2019.
Drawings
The drawings filed 04/13/2022 are acceptable.
Specification
The amendment to the specification filed 04/13/2022 is acceptable.
Information Disclosure Statement(s)
The two (2) information disclosure statement (IDS) document(s) submitted is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS document(s) has/have been fully considered by the examiner.
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 7-13 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.
Guidance Step 1:
The instant invention (claim 7 being representative) is directed to a method that performs a process. Thus, the claims are directed to one of the statutory categories of invention. MPEP 2106.03.
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. In this case, the claimed steps that are part of the abstract idea are as follows:
accessing data corresponding to a plurality of biological samples, the accessed data including a nucleotide sequence of a pathogen for each of the plurality of biological samples;
generating, based on the accessed data, an interactive dendrogram comprising an interactive portion that depicts a set of user-interface elements, wherein each user-interface element of the set of user-interface elements represents a biological sample of the plurality of biological samples, and wherein the user-interface elements in the set are arranged within the interactive portion based on a similarity of the nucleotide sequences of the biological samples that are respectively represented by the set of user-interface elements;
identifying a first subset of biological samples associated with the first biological sample corresponding to the user-interface element, wherein each biological sample of the first subset is identified based on a determination that a number of variations between the nucleotide sequences of the biological samples of the first subset and the first biological sample is within a threshold;
Mental Processes
Under the broadest reasonable interpretation, the above italicized steps amount to observing and manipulating/organizing data (e.g. using a dendrogram which is nothing more than a tree diagram). Notably, the claims do not impose any boundaries on how the italicized functions are actually being achieved. In addition, the instant specification describes using algorithms to perform at least some of the claimed functions [page 20]. As such, the specification provides sufficient evidence that the claims are directed to an abstract idea since the specific descriptions provided for accomplishing these tasks include only data reception and analysis. It is noted that the claim does not comprise any computer processor or hardware in order to perform the claimed steps. MPEP 2106.04(a)(2) also teaches examples of mental processes that include: An application program interface for extracting and processing information from a diversity of types of hard copy documents – Content Extraction, 776 F.3d at 1345, 113 USPQ2d at 1356. Accordingly, the above steps clearly fall within the mental process groupings 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].
It is additionally noted that MPEP 2106.04(a)(1) provides examples of claims that do not recite abstract idea, including: vi. a method of rearranging icons on a graphical user interface (GUI) comprising the steps of: receiving a user selection to organize each icon based on the amount of use of each icon, determining the amount of use of each icon by using a processor to track the amount of memory allocated to the application associated with the icon over a period of time, and automatically moving the most used icons to a position in the GUI closest to the start icon of the computer system based on the determined amount of use. However, these limitations are not analogous to the instant claims.
Mathematical Concept
In addition, the step of generating an interactive dendrogram wherein elements are “based on a similarity of…nucleotide sequences” amounts to mathematically relating data. Moreover, the artisan would recognize that “similarity” is intended a mathematical relationship and this position is supported by applicant’s own specification (which teaches hierarchical clustering algorithms for achieving the claimed results (page 20). Notably, the grouping of “mathematical concepts” in the 2019 PEG is not limited to formulas or equations, as words used in a claim operating on data to solve a problem can serve the same purpose as a formula. Therefore, when read in light of applicant’s own specification, the claimed steps clearly encompass mathematical relationships under the Revised Guidance. For these reasons, the claims are directed to a mathematical concept which is a judicial exception. See MPEP 2106.04 and 2106.05(II), and October 2019 Update at Section I.B. For these reasons, the claims are directed to one or more judicial exceptions. [Step 2A, Prong 1: YES].
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application of the exception or whether the claim is “directed to” the judicial exception. This evaluation is performed by (1) identifying whether there are any additional steps/elements recited in the claim beyond the judicial exception, and (2) evaluating those additional steps/elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. See MPEP 2106.04(d). The additional steps/elements recited in the claim beyond the judicial exception are as follows:
causing a graphical user interface to display the interactive dendrogram;
receiving, via the interactive portion of the graphical user interface, a selection of a user- interface element corresponding to a first biological sample;
causing the graphical user interface to visually indicate user-interface elements that correspond to the biological samples in the first subset.
In this case, the above steps are recited at a high of generality and result in nothing more than outputting data and/or collecting data for use by the abstract idea. Accordingly, the above steps amount to insignificant extra-solution activity and are not indicative of an integration into a practical application. See MPEP 2106.05(g). Regarding the claimed “interface elements” and “graphical user interface”, these features are generically recited and merely used as tools to obtain information or display the abstract idea. Moreover, while the claim does not require a processor, applicant is reminded that “generic computer components such as a computer and database do not satisfy the inventive concept requirement.” See MPEP 2106.05(f) and 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).
Examples that the courts have indicated may be sufficient to show an improvement in existing technology include: viii. A specific, structured graphical user interface that improves the accuracy of trader transactions by displaying bid and asked prices in a particular manner that prevents order entry at a changed price, Trading Techs. Int’l, Inc. v. CQG, Inc., 675 Fed. App'x 1001 (Fed. Cir. 2017) (non-precedential); and
C. Guidance Step 2B:
This part of the eligibility analysis evaluates whether the claim as a whole amounts to significantly more than the recited exception i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. See MPEP 2106.05.
As discussed above, the non-abstract steps/elements amount to nothing more than insignificant extra-solution activity. Moreover, applicant’s own specification teaches that the computing environment for performing the claimed invention includes nothing more than conventional elements [0024-0025]. In addition, a review of the prior art teaches that methods for using a GUI to display data (e.g. in a dendrogram) were routine and conventional int the art. See, e.g. Pavlopoulos et al. (BioData Mining 2010, 3:1 , pp.1-24; entire).Therefore, even upon reconsideration, there is nothing unconventional with regards to the above non-abstract elements/steps. See MPEP 2106.05(d)(Part II). Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
D. Dependent Claims
Dependent claims 8-13 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) 8, 10, 11, 12, these claims further limit the abstract idea or the nature of the data being used by the abstract idea. Accordingly, these claims are also directed to an abstract idea for the reasons set forth above (Step 2A, prong 1 analysis). Regarding claim(s) 9, 13, these claims further limit the nature of the GUI and therefore amount to insignificant extra-solution activity and are not indicative of an integration into a practical application for reasons discussed above (Step 2A, prong 2 and Step 2B analysis). See MPEP 2106.05(g). Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more.
Claim rejections - 35 USC § 112, 2nd Paragraph
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 7-13 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) 7 are also rejected due to said dependency.
Claim 7 recites an “interactive dendrogram comprising an interactive portion that depicts a set of user-interface elements…”. In this case, it is unclear what is meant by the term “interactive” such that the artisan would recognize what structural and/or functional limitation is intended. For example, the artisan would recognize that a GUI generated and display by a suitably programmed computer could typically include icons that can be clicked on by a user who is interacting with the GUI. However, in this case, the claimed method does not require a user and does not require a computer. A review of the specification does disclose a generic computer environment and hardware for performing the claimed invention [0024-0025] and various visual indications of interaction [0065]. However such limitations are not commensurate in scope with what is being claimed and it is improper to import narrowing limitations into the claims. MPEP 2111.01. Clarification is requested via amendment.
Claim 7 recites “wherein the user-interface elements…are based on a similarity of the nucleotide sequences”. In this case, it is unclear what positive process limitation is intended by the term “based on”. This limitation suggests an active method step (i.e. determining similarity) without explicitly requiring any such step. Applicant is reminded that limitation which suggest a particular process but do not explicitly require performing said process do not impose any limiting effect. See MPEP 2111.04. A review of the specification also does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. The specification does teach clustering algorithms [page 20] and a similarity interface [0033]. However, these features are not presently recited and it is improper to import narrowing limitations into the claims. MPEP 2111.01. As a result, it is unclear what computational techniques are included or excluded by the term “based on” such that one of ordinary skill in the art would know what computational limitations are intended. Clarification is requested via amendment.
Claim 7 recites “causing a graphical user interface to display the interactive dendrogram” and “causing the graphical user interface to visually indicate user-interface elements that correspond to the biological samples in the first subset.” In each case, it is unclear who or what is “causing” the claimed functions to be performed, e.g. a user, a computer/processor, or otherwise. Clarification is requested via amendment.
Claim 7 recites “receiving, via the interactive portion of the…interface, a selection of a user-interface element corresponding to a first biological sample”. Firstly, there is lack of antecedent basis for “the interactive portion of the graphical user interface.” No such portion has been previously presented or defined in the claim. Clarification is requested via amendment.
Secondly, it is unclear what positive process limitation is intended by the phrase “receiving…a selection of a user-interface element”, i.e. does the claim require receiving a particular type of data, selecting a particular type of data, or otherwise. Applicant is reminded that limitation which suggest a particular process but do not explicitly require performing said process do not impose any limiting effect. See MPEP 2111.04. A review of the specification also does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. As a result, it is unclear what computational techniques are included or excluded by the term “based on” such that one of ordinary skill in the art would know what computational limitations are intended. Clarification is requested via amendment.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 7-13 are rejected under 35 U.S.C. 103 as being unpatentable over Helfman et al. (US 20110074789 A1; Pub. Date: 03/31/2011) in view of Flygare et al. (Genome Biology (2016) 17:111, pp.1-18).
Regarding claim(s) 7, Helfman teaches an interactive dendrogram for analyzing and displaying biological sequence data [Abstract, 0055]. In particular, Helfman teaches functionality for clustering (accessing) data corresponding to biological sequences (i.e. samples) and accessing data from serves [Abstract, 0034, 0055; ref. claims 1, 15, 18; Figure 3].
Helfman teaches generating an interactive dendrogram based on the clustered data and displaying the dendrogram [ref. claims 1, 15, 18], wherein the sequence data can be hierarchically clustered based on similarities in the data, e.g., similar ranges of quantities, similar categories, etc. [0042] and wherein the dendrogram includes an interactive slider control element to adjust depth level [0009] , which at a minimum suggests generating an interactive dendrogram comprising an interactive portion, as claimed.
Helfman does not specifically teach using nucleotide sequences associated with a pathogen. However, the choice of data being used for analysis is nothing more than a design choice that does not change the function of the claimed process steps and Applicant has not disclosed that this particular feature provides an advantage, is used for a particular purpose, or solves a stated problem. Moreover, Flygare explicitly teaches interactive-based methods and GUIs for analyzing genomics sequence data that includes pathogen sequences [Abstract, Figure 1, and page 4, col. 1]. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to alter the method of Helfman by using pathogen sequences, as taught by Flygare, since both references teach the analysis of genomic sequence data using clustering and taxonomy-based tools. The motivation would have been to integrate the use of tree-based visualization tools for profiling microbial communities and identify similarities between pathogens.
Helfman teaches functionality for causing a GUI to display the interactive dendrogram, as set forth above [ref. claims 1, 15, 18].
Helfman teaches functionality for receiving a selection of a user-interface element (i.e. the slider) for adjusting depth level associated with clustered data [0006, 0009, 0042].
Helfman teaches a data analyzer for identifying patterns within the path data, i.e., similar or matching portions therein and outputting/displaying the results via the user interface [0048, 0049], which at a minimum suggests functionality for identifying sequences (i.e. samples) in the dendrogram based on variations.
Helfman teaches functionality for causing the GUI to visually indicate user-interface elements (i.e. sliders) that correspond to sequence data [0006, 0009, 0042], as set forth above.
Regarding claim(s) 8-13, the combination of Helfman and Flygare teaches or suggest all aspects of these claims for the following reasons.
Regarding claim(s) 9, Helfman teaches interactive dendrogram controls for analyzing and displaying biological sequence data [Abstract, 0055], which specifically includes a slider control that can be integrated with the dendrogram as a single interactive component in the form of a repositionable marker on the dendrogram to indicate the currently selected depth level of the dendrogram (i.e. threshold) [0006]. In such cases, receiving the selection of the depth of the dendrogram can comprise receiving an indication of a movement of the slider control and updating the page based on the selection of the depth of the dendrogram can comprise updating the detail view [0006].
Regarding claim(s) 8, 10, 11, 12, Helfman and Flygare do not specifically teach the claimed method further comprising receiving an indication to update threshold values to second values, wherein the values correspond to the extent of sequence variation. However, the choice of threshold being used to identify sequences (samples) is nothing more than a design choice that does not change the function of the claimed process steps and Applicant has not disclosed that this particular feature provides an advantage, is used for a particular purpose, or solves a stated problem. Moreover, Flygare teaches that taxonomic classification methods often require users to define arbitrary thresholds to derive final classifications [page 11, col. 1, “Conclusion”]. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date to have modified the teachings of Helfman and Flygare by updating threshold values, as claimed, since Flygare reasonably suggests this modification. One of ordinary skill in the art would have been able to perform this modification with a reasonable expectation of success since the dendrogram of Helfman allows for changing user defined values associated with sequence data (e.g. using the slider). The motivation would have been to allow users to customize the data visualization process.
Claims 7 and 13 are rejected under 35 U.S.C. 103 as being unpatentable over Pavlopoulos et al. (BioData Mining 2010, 3:1, pp.1-24) in view of Flygare et al. (Genome Biology (2016) 17:111, pp.1-18).
Regarding claim(s) 7, Pavlopoulos teaches computational methods for analyzing biological relationships between genomics data using tree analysis. In particular, Pavlopoulos teaches means for receiving accessing biological sequence data, and generating and displaying tree structures (i.e. dendrogram), clustering structures, and ontologies based on said data [see at least pages 2, 3, and 10-14; Figures 1 and 2]. In several embodiments (e.g. Dendroscope), users can interact with and manipulate the tree interactively: e.g. the mouse controls allow zooming in/out, rotation and dragging of the tree, subtree coloring, branch labeling, search and selection of a set of nodes and cluster generation results compatible to other applications [page 11-12]. In each case, the nodes of the tree are broadly interpreted as user-interface elements. Pavlopoulos also teaches applying a similarity criteria to the sequence data for visualization [page 18, ¶3]. Therefore, Pavlopoulos at a minimum suggests an interactive dendrogram comprising an interactive portion with user-interface elements as claimed, wherein user-elements (i.e. tree nodes) are based on sequence similarity.
Pavlopoulos does not specifically teach using nucleotide sequences associated with a pathogen. However, Flygare teaches interactive-based methods and GUIs for analyzing genomics sequence data that includes pathogen sequences [Abstract, Figure 1, and page 4, col. 1]. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to alter the method of Pavlopoulos by using pathogen sequences, as taught by Flygare, since both references teach the analysis of genomic sequence data using clustering and taxonomy-based tools. The motivation would have been to integrate the use of tree-based visualization tools for profiling microbial communities and identify similarities between pathogens.
Pavlopoulos teaches various computer platforms for displaying and manipulating visualization trees as set forth above [pages 11-14; Figures 1 and 2], which broadly reads on causing a GUI to display an interactive dendrogram.
Pavlopoulos teaches that users can interact with and manipulate the tree interactively, including selecting nodes associated with particular genomic data [page 11-12], and loading only the necessary parts of the graph into memory to improve performance [page 21, ¶2], which collectively teaches different embodiments for receiving a selection corresponding to a biological sample (via the interactive portion of the GUI).
Pavlopoulos does not specifically teach identifying a first subset of biological samples associated with the first biological sample corresponding to the user-interface element, wherein each biological sample of the first subset is identified based on a determination that a number of variations between the nucleotide sequences of the biological samples of the first subset and the first biological sample is within a threshold. However, Pavlopoulos makes obvious this feature by teaching distance and similarity matrixes [pages 8, 14] and a module (BioPerl) for identifying sequence distances based on pairwise alignment (i.e. variation) [page 19, Section 3], and since the artisan would know that calculated distances and similarities are values presentative of a threshold for identifying sequences.
Pavlopoulos additionally teaches various programs and toolkits for causing a GUI to display tree-based diagrams and elements that correspond to sequence data obtained from samples [pages 11-14; page 19, Sections 3, 4, and 5; Figures 1 and 2].
Regarding claim(s) 13, Pavlopoulos additionally teaches visually representing different elements of the tree using different color coding schemes [page 9, last ¶, page 11, last ¶, page 12, and Figure 1], which reads on user-interface elements with first and second colors.
Cited Prior Art
The following prior art made of record and not relied upon is considered pertinent to applicant' s disclosure.
Nozaki et al. (WO2001045026), which teaches methods for selecting a branch in a dendrogram, displaying a subtree including the selected branch and its leaves on a separate window, replacing the subtree with an icon, restoring the icon into the original subtree, and collecting and displaying keywords contained in the subtree.
Conclusion
No claims are allowed.
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
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