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 .
Claim Status
Claims 1-18 are currently pending and under exam herein.
Priority
The instant application is a Continuation of US 15/940,457, filed 29 March 2018, now US Patent 11,456,057. Priority for each of claims 1-18 is acknowledged to the EFD of 29 March 2018 herein.
Information Disclosure Statement
The Information Disclosure Statements filed 4 August 2022 and 25 September 2025 are in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS is included with this Office Action.
Drawings
The Drawings filed 4 April 2022 and replacements filed 16 December 2022 have been accepted. The Petition to Accept Color Drawings submitted 18 November 2022 has been granted under separate cover.
Specification
Note: All references to the Specification herein pertain to the PG publication: US20220399078A1.
Claim Rejections - 35 USC § 112(b)-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.
Claims 1-18 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1, 7, and 13 recite, “receiving a selection of a group of genomes; generating, by at least one processor, a heat map panel” wherein the claim is unclear with respect to the generation of the heat map panel because there is no indication as to the contents of the heat map panel. It would appear as if the claimed heat map panel is one that includes the data of the selection of a group of genomes, however, this is not claimed herein. As such, clarification is requested.
Claims 1, 7, and 13 recite, “displaying a visualization comprising the heat map panel”, wherein the claim is unclear with respect to what is being displayed as a visualization. Clarification is requested through clearer claim language such as, displaying the heat map comprising a taxonomic tree of genomic data (for example only and assuming that the heat map would be defined as such in previous claim steps).
Claims 1, 7, and 13 recite, “highlighting one or more genomes of the selected group in the heat map panel with a translucent overlay”, wherein there is insufficient antecedent basis in the claim for “one or more genomes of the selected group” as no group is actually “selected” in the claim. Rather, the claim is directed to only receiving data that is selection of a group of genomes. Clarification is requested.
Claims 1, 7, and 13 recite, “highlighting, based on the genome-genome distance, one or more additional genomes nearest to the one or more genomes with an additional translucent overlay”, wherein the claim is unclear with respect to the term “nearest”, as said term is a relative term which renders the claim indefinite. The term “nearest” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Clarification is requested.
Claims 2, 8, and 14 recite, “wherein the one or more additional genomes has the smallest genome-genome distance to the one or more genomes”, wherein the claim is unclear with respect to the term “smallest”, as said term is a relative term which renders the claim indefinite. The term “smallest” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Clarification is requested.
Claims 5, 11, and 17 recite, “further comprising: providing a metadata window for display in response to location of a pointer on the heat map panel, wherein the metadata window shows information about two genomes at the location”, wherein there is insufficient antecedent basis in the claim for “in response to location of a pointer on the heat map panel”, as no location for a pointer on the heat map panel was previously claimed. Clarification is requested.
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 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The instant rejection reflects the framework as outlined in the MPEP at 2106.04:
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture or composition of matter;
(2A) Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1 Analysis: Are claims directed to process, machine, manufacture/composition of matter
With respect to step (1): Claims 1-6 and 13-18 are directed to a method and a system.
Claims 7-12 are not directed to a proper class of invention (either process, machine, manufacture/composition of matter) because said claims recite “a computer program product”. Therefore the claims read on carrier waves which are non-statutory which read on transitory propagating signals which are not proper patentable subject matter because they do not fit within any of the four statutory categories of invention (In re Nuijten, Federal. Circuit, 2006). It is noted that the recitation of a "non-transitory computer-readable medium" would overcome the rejection as pertains to this matter. However, the claims would still be subject to the rejections below and are included herein for purposes of compact prosecution, under the assumption that amendment is forthcoming.
Step 2A, Prong 1 Analysis: Do claims recite abstract idea
With respect to step (2A)(1), the claims recite abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the (2A)(1) evaluation, the claims are found herein to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and in conjunction with mathematical concepts (in particular mathematical relationships).
The claim steps to abstract ideas are as follows:
Claims 1, 7, and 13: generating, by at least one processor, a heat map panel; highlighting one or more genomes of the selected group in the heat map panel with a translucent overlay; measuring genome-genome distance between the one or more genomes; and highlighting, based on the genome-genome distance, one or more additional genomes nearest to the one or more genomes with an additional translucent overlay, wherein steps directed to generating a het map panel are nothing more that making selections of data and using a computer as a tool to perform color coordination (heat map). One could also do this via colored pencil, as there are no steps to further detail the elements of said generation and under the Broadest Reasonable Interpretation (BRI) of the claim this claim step is abstract. This is true of the steps of highlighting, also under the BRI which is a step that can be done mentally with pen and paper and by overlaying a translucent piece of material. Further steps directed to highlighting another genome is similarity an abstract step.
Dependent claims herein further limit the abstract steps such as in claims 2, 8, and 14 further distance; claims 3, 9, and 15 directed to highlighting; claims 4, 10, and 16 directed to highlighting; claims 6, 12, and 18 including taxonomic tree visualization that is a mental operation.
Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined herein to each cover performance either in the mind (calculations by hand or pen and paper) and/or performance by mathematical operation (taxonomy). The instant claims are analogous to an abstract idea in the form of at least a mental process, at least equivalent to a computer-implemented process, including obtaining and comparing intangible data (e.g. Cybersource, Synopsys and Electric Power Group). Under the BRI herein, it is not clear that the claim embodiments are limited so as to require complexity precluding analogy to a mental process. One could simply, for example, perform said operation with pen and paper, or, alternatively with the aid of a generic computer as a tool to perform said calculations. These recitations are similar to the concepts of collecting information, analyzing it and providing certain results from the collection and analysis (Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations (Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in (Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind with pen and paper, and can include mathematical concepts.
Further, see MPEP § 2106.04(a)(2), subsection III. The courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation (see, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674: noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1139, 120 USPQ2d 1473, 1474 (Fed. Cir. 2016): holding that claims to a mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper"). Nor do the courts distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind" (see Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016): holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer").
Step 2A, Prong 2 Analysis: Integration to a Practical Application
Because the claims do recite judicial exceptions, direction under (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the following additional elements:
Claims 1, 7, and 13: receiving a selection of a group of genomes; displaying a visualization comprising the heat map panel; computer; processor; system; memory
Claims 5, 11, and 17: providing a metadata window for display in response to location of a pointer on the heat map panel, wherein the metadata window shows information about two genomes at the location
Further with respect to the additional elements in the instant claims, those steps directed to data gathering (receiving selection of a group of genomes) perform functions of collecting the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or on how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application. (MPEP 2106.05(g).
Further, the system, processor, memory, instructions, and window display are part of a general purpose computer system and there are no details herein wherein of how the specific computer structures are used to implement the judicial exceptions beyond generic computing operations, i.e., the computer elements of the claims do not provide improvements to the functioning of the computer itself (see: DDR Holdings, LLC v. Hotels.com LP); they do not provide improvements to any other technology or technical field (see: Diamond v. Diehr); nor do they utilize a particular machine (see: Eibel Process Co. v. Minn. & Ont. Paper Co.). Hence, these are mere instructions to apply the judicial exception using a computer, and therefore the claim does not provide integration into a practical application of any judicial exception.
Step 2B Analysis: Do Claims Provide an Inventive Concept
The claims are lastly evaluated using the (2B) analysis, wherein it is determined that because the claims recite abstract ideas, and do not integrate that abstract ideas into a practical application, the claims also lack a specific inventive concept. Applicant is reminded that the judicial exception alone cannot provide the inventive concept or the practical application and that the identification of whether the additional elements amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, receiving data in the form of genomes for display is a well-understood, routine and conventional activity. For example, the prior art to Arakawa et al. (BMC Bioinformatics (2009) Vol. 3;10 pages) disclose molecular biology data scaled into layers that include data such as genome, proteome, metabolome, biochemical pathways and the like (abstract). Further, the prior art discloses genome data in the context of map generations (p. 2). Further the prior art to Babiki et al. (Nucleic Acids Research (2016) Vol. 44:W147-W153-IDS reference) discloses getting various data for heatmapping applications, such as molecular biological data (p. W147).
With respect to the claims to the system and processor, memory and instruction, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. Further, the specification discloses that computer processors and systems, as example, are generic computing systems [0083]-[0093]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than an abstract idea (see MPEP 2106.05(b)I-III).
The dependent claims have been analyzed with respect to step 2B and none of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception.
For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
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.
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.
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.
1. Claims 1-18 are rejected under 35 U.S.C. 103 as being unpatentable over Arakawa et al. (BMC Bioinformatics (2009) Vol. 3;10 pages) in view of Zhao et al. (Biomed Research International (2014) Vol. 2738:6 pages).
Claims 1, 7, and 13 are directed to a method, computer program product, and system, including steps of:
receiving a selection of a group of genomes;
generating, by at least one processor, a heat map panel;
displaying a visualization comprising the heat map panel;
highlighting one or more genomes of the selected group in the heat map panel with a translucent overlay;
measuring genome-genome distance between the one or more genomes; and
highlighting, based on the genome-genome distance, one or more additional genomes nearest to the one or more genomes with an additional translucent overlay.
The prior art to Zhao et al. discloses the heatmap tool package, Heatmap3 (receiving a selection of a group of genomes; generating, by at least one processor, a heat map panel; displaying a visualization comprising the heat map panel) (abstract; p.2, col. 1). Zhao et al. disclose displaying visualization and ability to run distance methods over a set and including a wide range of color selections (highlights) (displaying a visualization comprising the heat map panel; highlighting one or more genomes of the selected group in the heat map panel with a translucent overlay; measuring genome-genome distance between the one or more genomes; and highlighting, based on the genome-genome distance, one or more additional genomes nearest to the one or more genomes with an additional translucent overlay) (p.2, col. 1; Figure 1; p.3).
With respect to claims 2, 8, and 14, Zhao et al. disclose “the "heatmap3" package also provides an option which allows the generation of multiple heat maps and dendrograms based on the threshold criteria selected by the user. Using the same dataset, we performed heat map and cluster analysis using all genes, the top 3000 genes, and the top 500 genes selected by standard deviation. Figure 2 shows the three dendrograms. All three dendrograms showed clearly two large clusters. Using TN status as the primary phenotype, each time a more stringent standard deviation cutoff was used, the clusters became clearer between TN and non-TN. This example illustrates the importance of selecting more statistically varied genes for subtyping purposes” (p.3)
Zhao et al. do not specifically include that a group of genomes is received as in claims 1, 7, and 13 nor do they specifically include that genomes are highlighted simultaneously or one at time per se. Further, functionality does not specifically include a metawindow and zoom and scan (claims 3-6, 9-12, 15-18).
However the prior art to Arakawa et al. disclose, “Genome Projector is developed with G-language Genome Analysis Environment version 1.8.4 [13-15] with Ext-JS framework 1.0.1 for Web interfaces using the AJAX Web programming paradigm [16] and Google Maps API [17] for ZUI. Google Maps API was chosen for ZUI because of its high performance, ability to zoom with mouse scroll wheel operation, and popularity, so that users are already accustomed to the interface and therefore can navigate intuitively”. Further, said operations are directed to genome scale projection and large images of genome maps (p. 2). Position and coordinates of genomes as well as search ability within are also disclosed (p. 2), as well as zoom and scan function (p. 3) and overlay layering (Figure 4).
As such, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the Genome Projector as disclosed in Arakawa et al. with the functionality of heatmap3, as disclosed in Zhao et al. with a reasonable expectation of success, because Arakawa et al. disclose that Genome Projector is useful as a gateway to multi-scale and multi-layered -omic information and is easily integrable (abstract; p.9). As both references are in the same filed of endeavor, said invention is further obvious.
Prior Art Made of Record
The following prior art made of record and not relied upon is considered pertinent to applicant’s disclosure:
1. Fernandez et al. (Scientific Data (2017) Vol. 4:12 pages) disclosing a zoom, pan search, select and animate visualization tool, Clustergrammer, for heatmap visualization.
Conclusion
No claims are allowed.
Parent application, now US Patent 11,456,057, has been assessed for double patenting. At this time, the claims are not overlapping and not obvious variants of each other.
E-mail Communications Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting following form via EFS-Web or Central Fax (571-273-8300): PTO/SB/439. Applicant is encouraged to do so as early in prosecution as possible, so as to facilitate communication during examination.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
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/Lori A. Clow/Primary Examiner, Art Unit 1687