DETAILED ACTION
Notice of 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 .
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 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.
Preliminary Amendment
The preliminary amendment filed on 06/29/2026 was not entered because entry of the amendment would unduly interfere with the preparation of the Office action. See 37 CFR 1.115(b)(2). The examiner spent a significant amount of time on the preparation of an Office action before the preliminary amendment was received. On the date of receipt of the amendment, the examiner had completed the drafting of the Office action and was waiting for the supervisory patent examiner’s approval.
Furthermore, entry of the preliminary amendment would require significant additional time on the preparation of the Office action. Specifically, entry of the preliminary amendment would require the examiner to revise the Office action extensively to address the new issues raised and the new claims added in the preliminary amendment.
A responsive reply (under 37 CFR 1.111 or 37 CFR 1.113 as appropriate) to this Office action must be timely filed to avoid abandonment.
If this is not a final Office action, applicant may wish to resubmit the amendment along with a responsive reply under 37 CFR 1.111 to ensure proper entry of the amendment. Claims filed on 06/09/2023 are examined.
Status of the Claims
Claims 4, 8-9, 12, 15, 18, 21 and 23-52 are canceled.
Claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57 are pending.
Claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57 are rejected.
Priority
This application No. 18/118,630 (03/07/2023) claims priority from US Application No. 63/317,950 (03/08/2022), as reflected in the filing receipt mailed on 07/06/2023. The claims to the benefit of priority are acknowledged and the effective filing date of claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57 is 03/08/2022.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 01/16/2024, 04/02/2024, 11/19/2025 and 03/02/2026 were 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 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57 are rejected under 35 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 §I). Abstract ideas include mathematical concepts and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)).
101 background
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Analysis of instant claims
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The instant claims are directed to a method (claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57) which falls within one of the categories of statutory subject matter.
[Step 1: claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Background
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Analysis of instant claims
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mathematical concepts (in particular mathematical relationships and formulas) and mental processes (in particular procedures for observing, analyzing and organizing information are as follows.
Mathematical concepts (in particular mathematical relationships and formulas) include:
• "visually aligning each layer along the multi-dimensional model relative to a corresponding amino acid sequence for each layer" (claim 19).
The claim identified above read on math. The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation and determined each element performed by mathematical operation. The step directed to “executing an alignment algorithm involving layers of a multidimensional model and generating an output of such alignment step” requires mathematical techniques as the only supported embodiments because it describes a mathematical technique (MPEP 2106.04(a)(2) pertains). An alignment algorithm is capable of displaying a visual represent of the alignment. Further support for the mathematical techniques used in the claims is provided in the specification at [0036], which discloses computer elements comprising digital layers. Thus, the recited terms correspond to verbal equivalents of mathematical concepts because they constitute actions executed by a group of mathematical steps in a form of a mathematical algorithm; thus mathematical concepts (MPEP 2106.04(a)(2)). A mathematical concept need not be expressed in mathematical symbols, because "words used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). MPEP 2106.04(a)(2) pertains.
Mental processes, defined as concepts or steps practically performed in the human mind such as steps of observations, evaluations, judgments, analysis, opinions or organizing information include:
• "displaying the sequence infographic aligned relative to a plurality of sequence infographics" (independent claim 1);
• "detecting an input indicating a movement of a bounding element related to the amino acid sequence area of interest, wherein the bounding element represents an amino acid bounding value" (claim 7);
• "visually distinguishing each sequence infographic of the plurality of sequence infographics as a layer of the multi-dimensional model" (claim 17); and
• "visually distinguishing an amino acid sequence area of interest within the dynamic amino acid sequence filter element based on a position of the at least one movable bounding indicator on the dynamic amino acid sequence filter element corresponding to the particular amino acid" (claim 53).
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind (i.e. concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) or because the method only requires a user to manually determine action based on an added number. Under the BRI, the recited limitations are mental processes because a human mind is also sufficiently capable of: evaluate sequences previously aligned and draw it out in the mind; evaluate input data to detect a specific feature; aligning would probably be better identified as math, because it has to do with multidimensional data, but positioning the indicator seems like a mental action to me - it's just pointing out a part of the sequence, right?
Dependent claims 13 recites further details about the displaying the sequence infographic step. "The display of an abstract idea (i.e., example of the abstract idea being displayed) is considered to recite that same abstract idea (see Interval Licensing LLC v AOL, Inc., 896 F.3d 1335, 1344-45 (Fed. Cir. 2018), which recognized that information “is an intangible” and that “the collection, organization, and display of two sets of information on a generic display device is abstract absent a specific improvement to the way computers operate”).
[Step 2A Prong One: claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57: Yes ]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Background
MPEP 2106.04(d).I 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).
Analysis of instant claims
Instant claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57 recite additional elements that are not abstract ideas:
• "computer-implemented" (claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57);
• "generating an antibody product listing within the graphical user interface, responsive to a user interaction , wherein the antibody product listing includes at least one antibody product including corresponding sequence information and product specifications" (independent claim 1);
• "generating a sequence infographic based on the corresponding sequence information, wherein the sequence infographic includes an amino acid sequence area of interest indicator" (independent claim 1);
• "updating the antibody product listing within the graphical user interface responsive to the input by excluding antibody products with at least one amino acid sequence range value outside the amino acid bounding value, wherein the bounding element includes a slider visually positioned on an interval representing values of the amino acid sequence range" (claim 7);
• "generating a three-dimensional model of the sequence infographic including the amino acid sequence area of interest indicator" (claim 16)
• "generating a multi-dimensional protein model representing the plurality of sequence infographics" (claim 17);
• "generating a multi-dimensional protein model including a visual representation of at least one level of protein structure, wherein the at least one level of protein structure includes one of a primary protein structure, a secondary protein structure, a tertiary protein structure and a quaternary protein structure" (claim 20);
• "generating a dynamic amino acid sequence filter element including at least one movable bounding indicator, wherein the dynamic filter element visually represents an amino acid sequence range of a given target protein, and wherein the at least one movable bounding indicator visually represents a particular amino acid within the amino acid sequence range" (claim 53); and
• "updating an antibody product listing within the graphical user interface responsive to a user input by excluding antibody products with at least one amino acid sequence range value outside the amino acid sequence area of interest" (claim 54).
Dependent claims 2-3, 5-6 and 14 recite further details about the sequence infographic. Dependent claims 10-11 recite further details about the location of the slider on the interval. Dependent claim 55 recites further details about the at least one movable bounding indicator. Dependent claims 56-57 recite further details about the generating a dynamic amino acid sequence step.
Considerations under Step 2A, Prong Two
The recited limitations in claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57 are interpreted as requiring the use of a computer. Hence, the claims explicitly recite steps executed by computers and therefore can be described as computer functions or instructions to implement on a generic computer.
Further steps directed to additional non-abstract elements of a computing device/computer do not describe any specific computational steps by which the "computer parts" perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions.
The judicial exceptions in the claims are considered to perform the claimed abstract idea with a computer, which is not sufficient to integrate an abstract idea into a practical application (see MPEP 2106.05(f)); since steps that can be performed mentally and merely performing the mental process in a computer environment do not negate the fact that something that can be carried out in the human mind. See MPEP 2106.04(a)(2).III.C.
The recited "updating the antibody product listing within the graphical user interface responsive to the input" read on data gathering activities based on user input; not amounting to a practical application. The type of data doesn’t change that it is mere data gathering or conventional computer receiving means.
Claims directed to "generating an antibody product listing within the graphical user interface, responsive to a user interaction"; "generating a sequence infographic based on the corresponding sequence information"; "generating a three-dimensional model of the sequence infographic"; "generating a multi-dimensional protein model representing the plurality of sequence infographics"; "generating a multi-dimensional protein model including a visual representation"; and "generating a dynamic amino acid sequence filter …to visually represent an amino acid sequence" are interpreted as data outputting and as such insignificant extra-solution activity. Claims reciting " visual representation/visually representing" the generated output described above are interpreted as data output and as such insignificant extra-solution activity.
There are no additional limitations to indicate that the claimed computer, processor, or computer readable medium require anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(b).
Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)).
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements. Additional elements are further discussed in Step 2B below.
Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
[Step 2A Prong Two: claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during examination 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).
Claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57 recite a computer or computer functions, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions; which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
Further, the courts have found that and outputting data is a well-understood, routine, and conventional function of a computer when claimed in a generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versa ta Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(Il)(i)).
With respect to the instant claims, the prior art review to O'donoghue ("Visualization of macromolecular structures." Nature methods 7.Suppl3:S42-S55 (2010)); newly cited) discloses that generating a multi-dimensional protein within the graphical user interface responsive to a user input is routine, well-understood and conventional in the art. Said portions of the prior art are, for example, pg. S43 Table 1.
When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a broad technological environment. See MPEP 2106.05(a) and 2106.05(h).
The instant claims constitute insignificant extra solution activity, and when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(g)). Hence, these elements, when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(d)).
[Step 2B: claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57: No]
Conclusion: Instant claims are directed to non-statutory subject matter
For the reasons above, the claims in this instant application, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept not clearly anything significantly more.
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 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, 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 negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under pre-AIA 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.
A. Claims 1-3, 5-6, 13-14, 16-17 and 19 are rejected under 35 U.S.C. 103(a) as being unpatentable over Beaver ("EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB)." Immunome research 3(1):3 (2007)) in view of Timlin ("Web Based Multidimensional Interactive Visualizations as Supplemental Material for Biological Research Articles." (2017)), as cited on the attached Form PTO-892.
Claim 1 recites:
generating an antibody product listing within the graphical user interface, responsive to a user interaction, wherein the antibody product listing includes at least one antibody product including corresponding sequence information and product specifications;
generating a sequence infographic based on the corresponding sequence information, wherein the sequence infographic includes an amino acid sequence area of interest indicator; and
displaying the sequence infographic aligned relative to a plurality of sequence infographics
• Beaver teaches EpitopeViewer - a platform-independent Java application for the visualization of the three-dimensional structure and sequence (i.e. visual evaluation of sequence information) of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules) (i.e. generating an antibody product listing within the graphical user interface, responsive to a user interaction, wherein the antibody product listing includes at least one antibody product including corresponding sequence information and product specifications) (pg. 1 Abstract); wherein viewer is used by an user to use the tools via an application downloaded to their client computer (i.e. interactive graphical user interface) (pg. 2 col. 2 para. 1); wherein the contact window provides a 2D plot of interactions between epitope and receptor residues (i.e. generating a sequence graphics based on the corresponding sequence information, wherein the sequence infographic includes an amino acid sequence area of interest indicator) (pg. 2 col. 2 para. 5) (pg. 3 col. 1 para. 1); wherein epitopes inferred from 3D structures of antigens in complexes with immune receptors can be retrieved and displayed in the EpitopeViewer from the IEDB web-site i.e. (i.e. displaying the sequence graphics aligned relative to a plurality of sequence graphics) (pg. 5 col. 2 para. 2); wherein the 3D structure view can be saved in a variety of graphics formats using the "Save 3D Image" button on the right control panel of the viewer (pg. 2 col. 2 para. 3).
• Beaver does not teach "sequence infographics." However, Timlin teaches a multidimensional web based interactive visualization created using JavaScript and the D3.js library (pg. 15 para. 1); wherein protein systems can be visualized in such a way as to allow for easier exploration (pg. 9 para. 2); wherein how textual information can be translated from a JSON file to an infographic (i.e. reading on sequence infographics) (pg. 15 para. 1); wherein a phylogenetic tree graphic is manipulatable by the user (pg. 37 para. 3); wherein graphics of data on the action of antibodies under specific conditions is displayed using a dot plot with each data point being represented as a colored shape (pg. 38 para. 3).
Claim 2 recites:
wherein the amino acid sequence area of interest indicator includes an epitope indicator shown relative to the sequence amino acid sequence area of interest indicator
• Beaver teaches the viewer's contact window provides a 2D plot of interactions between epitope and receptor residues (i.e. includes an epitope indicator shown relative to the sequence amino acid sequence area of interest indicator) (pg. 2 col. 2 para. 5) (pg. 3 col. 1 para. 1).
Claim 3 recites:
wherein the sequence infographic includes a base layer representing an amino acid sequence range of a given target protein, a second layer representing the amino acid sequence area of interest indicator that includes visual elements related to data points in the amino acid sequence range of the given target protein, and a third layer representing an epitope
• Beaver teaches EpitopeViewer - a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules) (pg. 1 Abstract); wherein immune receptor residues (i.e. given target protein) interacting with the epitope are displayed by default (i.e. data representing an amino acid sequence range of a given target protein) (pg. 4 col. 1 para. 4); wherein interactions between epitope and immune receptor are calculated by the viewer on-the-fly and provided for both curated and calculated receptor residues interacting with the epitope with salt bridges (or ion pairs) identified for the charged side-chain atoms (i.e. indicator that includes visual elements related to data points in the amino acid sequence range of the given target protein) (pg. 4 col. 2 para. 1); wherein the 3D structure window provides a renderable view of the structure of the immunological complex (Fig. 1), epitope and immune receptor residues interacting with epitope in an all-atom representation (i.e. data representing an epitope) (pg. 2 col. 2 para. 3).
• Beaver does not teach "the sequence infographic including multiple information layers." However, Timlin teaches that displaying information on a map can be done by varying shapes of different sizes or symbols representing different objects or data can be used to add multiple layers of information in a single data point (pg. 4 para. 1); wherein multidimensionality and unidimensionality refer to the number of layers (i.e. unidimensionality reading on one layer and multidimensionality reading on at least two layers) and the number of different types of graphics used to display information and the amount of different information represented (pg. 8 para. 1).
Claim 5 recites:
wherein the visual elements include at least one of a first visual indicator representing a specific data point, a second visual indicator representing an interval between two data points, a third visual indicator representing an estimated data point, a fourth visual indicator representing an estimated interval including at least one estimated data point
• Beaver teaches 3D-visualization of curated interactions between epitope and receptor as well as derived van der Waals and hydrophobic interactions calculated on-the-fly (i.e. visual indicator representing an estimated data point) including contacting residues, atoms and contact distances (i.e. visual indicator representing an estimated interval including at least one estimated data point) (pg. 5 col. 1 para. 3); wherein in deriving hydrophobic interactions that two atoms are assumed to be involved in hydrophobic interaction if they are separated from each other by a distance ≤ 5.0 Å (i.e. visual indicator representing an estimated interval) (pg. 4 col. 2 para. 1); wherein it is assumed that negatively charged side-chain atoms of amino acids Asp Glu are capable of forming salt bridges with positively charged side-chain atoms of amino acids Arg, Lys and His within a 4Å distance (i.e. visual indicator representing an interval between two data points) (pg. 4 col. 2 para. 1).
Claim 6 recites:
wherein the amino acid sequence area of interest indicator represents at least one of a particular amino acid sequence value, an amino acid sequence range of values, an amino acid sequence starting value, an amino acid sequence ending value, and an amino acid sequence intermediate value
• Beaver does not teach the recitation above. However, Timlin teaches sequence logos that use size, color, and arrangement to allow the viewer to pull out information beyond the literal text sequence such as frequency of nucleotides or amino acids, information content at certain positions, and can highlight conserved or important regions of a sequence (i.e. reading on indicator of amino acids positions that begin a sequence – hence starting value – and amino acids positions in intermediate and terminal regions – hence intermediate and ending values) (pg. 6 para. 1).
Claim 13 recites:
wherein displaying further comprises aligning each sequence infographic of the plurality of sequence infographics along the visual representation of the amino acid sequence range of the given target protein
• Beaver does not teach the recitation above. However, Timlin teaches that multidimensional web based interactive arrangement to allow the viewer to pull out information beyond the literal text sequence such as frequency of nucleotides or amino acids, information content at certain positions, and can highlight conserved or important regions of a sequence wherein in the graphic, the different amino acids or nucleotides that may appear at any given position are stacked on top of each other with each type represented by a different color as well as its letter abbreviation (pg. 6 para. 1).
Claim 14 recites:
wherein the sequence infographic enables visual evaluation of the sequence based on at least one of sequence size, sequence position, and sequence overlap
• Beaver does not teach the recitation above. However, Timlin teaches that multidimensional web based interactive arrangement to allow the viewer to pull out information beyond the literal text sequence such as frequency of nucleotides or amino acids, information content at certain positions, and can highlight conserved or important regions of a sequence wherein in the graphic, the different amino acids or nucleotides that may appear at any given position are stacked on top of each other with each type represented by a different color as well as its letter abbreviation (pg. 6 para. 1).
Claim 16 recites:
wherein generating the sequence infographic further comprises generating a three-dimensional model of the sequence infographic including the amino acid sequence area of interest indicator
• Beaver does not teach the recitation above. However, Timlin teaches a multidimensional web based interactive visualization (i.e. reading on a three-dimensional model) (pg. 15 para. 1); demonstrating how textual information can be translated to an infographic (pg. 15 para. 1); wherein graphics of data on the action of antibodies under specific conditions is displayed using a dot plot with each data point being represented as a colored shape (pg. 38 para. 3); wherein the arrangement allow the viewer to pull out information beyond the literal text sequence such as frequency of nucleotides or amino acids, information content at certain positions, and can highlight conserved or important regions of a sequence (pg. 6 para. 1).
Claim 17 recites:
further comprising; generating a multi-dimensional protein model representing the plurality of sequence infographics: and visually distinguishing each sequence infographic of the plurality of sequence infographics as a layer of the multi-dimensional model
• Beaver does not teach the recitation above. However, Timlin teaches a multidimensional web based interactive visualization (pg. 15 para. 1); demonstrating how textual information can be translated to an infographic (pg. 15 para. 1); wherein graphics of data on the action of antibodies under specific conditions is displayed using a dot plot with each data point being represented as a colored shape (pg. 38 para. 3); wherein the arrangement allow the viewer to pull out information beyond the literal text sequence such as frequency of nucleotides or amino acids, information content at certain positions, and can highlight conserved or important regions of a sequence (i.e. visually distinguishing each sequence infographic of the plurality of sequence infographics as a layer of the multi-dimensional model) (pg. 6 para. 1).
Claim 19 recites:
further comprising visually aligning each layer along the multi-dimensional model relative to a corresponding amino acid sequence for each layer
• Beaver does not teach the recitation above. However, Timlin teaches displaying information on a map can be done by varying shapes of different sizes or symbols representing different objects or data can be used to add multiple layers of information in a single data point (pg. 4 para. 1); wherein multidimensionality and unidimensionality refer to the number of layers and the number of different types of graphics used to display information and the amount of different information represented (i.e. visually aligning each layer along the multi-dimensional model relative to a corresponding amino acid sequence for each layer) (pg. 8 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 1-3, 5-6, 13-14, 16-17 and 19, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Beaver in view of Timlin because all references disclose methods for visualizing amino acid sequences. The motivation would have been to allow multiple pages of different graphics to be easily be accessed and explored on a single multidisciplinary interactive visualization (pg. 1 Abstract Timlin) and apply it to many areas of industry, art, business, government and science use interactive visualizations including some fields of biology such as systems biology and genomics (pg. 1 para. 1 Timlin).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the visualizing amino acid sequences method of Beaver to the methods by Timlin because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for visualizing amino acid sequences.
B. Claims 7 and 10-11 are rejected under 35 U.S.C. 103(a) as being unpatentable over Beaver and Timlin as applied to claim 1 above further in view of Elmqvist ("Rolling the dice: Multidimensional visual exploration using scatterplot matrix navigation." IEEE transactions on Visualization and Computer Graphics 14(6):1141-1148 (2008)) in view of Jehl ("ProViz—a web-based visualization tool to investigate the functional and evolutionary features of protein sequences." Nucleic acids research 44.W1:W11-W15 (2016)), as cited on the attached Form PTO-892.
Claim 7 recites:
detecting an input indicating a movement of a bounding element related to the amino acid sequence area of interest, wherein the bounding element represents an amino acid bounding value: and
updating the antibody product listing within the graphical user interface responsive to the input by excluding antibody products with at least one amino acid sequence range value outside the amino acid bounding value, wherein the bounding element includes a slider visually positioned on an interval representing values of the amino acid sequence range
• Beaver teaches EpitopeViewer - a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules) (i.e. visualization of elements related to the amino acid sequence area of interest) (pg. 1 Abstract).
• Neither Beaver or Timlin teach "detecting an input indicating a movement of a bounding element related to the area of interest, wherein the bounding element represents an bounding value." However. Elmqvist teaches an interactive methods to explore multidimensional data using scatterplots for interactive navigation (i.e. interactive graphical user interface) in the multidimensional space; wherein transitions between scatterplots are performed as animated rotations in 3D space and users can iteratively build queries using bounding volumes in the dataset (i.e. user can vary bounding values for datapoints in a dataset), sculpting the query from different viewpoints to become more and more refined (pg. 1141 Abstract); wherein all navigation operations are restricted to orthogonal movement and are atomic transactions in that they never leave the main scatterplot visualization in an intermediate stage—when the user stops interacting, the visualization settles into one of the 2D scatterplots in the scatterplot matrix (i.e. detecting an input indicating a movement of a bounding element related to the area of interest, wherein the bounding element represents an bounding value) (pg. 1144 col. 1 para. 1).
• Neither Beaver or Timlin teach "updating the antibody product listing within the graphical user interface responsive to the input by excluding antibody products with at least one amino acid sequence range value outside the amino acid bounding value, wherein the bounding element includes a slider visually positioned on an interval representing values of the amino acid sequence range." However, Jehl teaches a browser-based visualization tool to display protein features from precomputed multiple sequence alignments; wherein features are retrieved in an automated manner from resources describing protein modular architecture, post translational modification, structure, sequence variation and experimental characterization of functional regions (pg. W11 Abstract); wherein users can directly specify a range of residues, move a slider or ctrl + click on a feature to select a target area and the selected area can be used to resize or highlight the visualization (i.e. updating the antibody product listing within the graphical user interface responsive to the input by excluding antibody products with at least one amino acid sequence range value outside the amino acid bounding value, wherein the bounding element includes a slider visually positioned on an interval representing values of the amino acid sequence range) (pg. W14 col. 2 para. 1).
Claim 10 recites:
wherein location of the slider on the interval indicates a bounding value in the amino acid sequence range of antibody products included in the antibody product listings
• Neither Beaver or Timlin teach the recitation above. However, Jehl teaches the visualization of the protein architecture showing key features of the protein: secondary structure, topology, globular domains, SLiMs and PTM sites (i.e. reading on a range of antibody products included in the antibody product listings); wherein users can move a slider or ctrl + click on a feature to rapidly navigate to the specific region of the main visualization (i.e. location of the slider on the interval indicates a bounding value in the amino acid sequence range) (pg. W14 col. 1 para. 1).
Claim 11 recites:
wherein moving the slider from a first location to a second location indicates a change from a first bounding value to a second bounding value
• Neither Beaver or Timlin teach the recitation above. However, Jehl teaches that users can move a slider or ctrl + click on a feature to rapidly navigate to the specific region of the main visualization (i.e. moving the slider from a first location to a second location indicates a change from a first bounding value to a second bounding value) (pg. W14 col. 1 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 7 and 10-11, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Beaver and Timlin in view of Elmqvist and Jehl because all references disclose methods for visualizing amino acid sequences. The motivation would have been to apply dimensions in the navigation space that can be reordered, manually or automatically, to highlight salient correlations and differences among them (pg. 1141 Abstract Elmqvist) and allow users with limited bioinformatic skills to rapidly access data pertinent to their research via visualizations customized with user defined data (pg. W11 Abstract Jehl).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the visualizing amino acid sequences method of Beaver and Timlin to the methods by Elmqvist and Jehl because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for visualizing amino acid sequences.
C. Claims 20 and 22 are rejected under 35 U.S.C. 103(a) as being unpatentable over Beaver and Timlin as applied to claim 1 above further in view of Jehl as cited on the attached Form PTO-892.
Claim 20 recites:
further comprising generating a multi-dimensional protein model including a visual representation of at least one level of protein structure, wherein the at least one level of protein structure includes one of a primary protein structure, a secondary protein structure, a tertiary protein structure and a quaternary protein structure
• Neither Beaver or Timlin teach the recitation above. However, Jehl teaches the visualization of the protein architecture showing key features of the protein: secondary structure, topology, globular domains, SLiMs and PTM sites; wherein users can move a slider or ctrl + click on a feature to rapidly navigate to the specific region of the main visualization (pg. W14 col. 1 para. 1).
Claim 22 recites:
further comprising positioning the amino acid sequence area of interest indicator on the at least one level of protein structure
• Neither Beaver or Timlin teach the recitation above. However, Jehl teaches the visualization of the protein architecture showing key features of the protein: secondary structure (i.e. at least one level of protein structure), topology, globular domains, SLiMs and PTM sites; wherein users can move a slider or ctrl + click on a feature to rapidly navigate to the specific region of the main visualization (i.e. positioning the amino acid sequence area of interest indicator on the at least one level of protein structure) (pg. W14 col. 1 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 20 and 22, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Beaver and Timlin in view of Jehl because all references disclose methods for visualizing amino acid sequences. The motivation would have been to allow users with limited bioinformatic skills to rapidly access data pertinent to their research via visualizations customized with user defined data (pg. W11 Abstract Jehl).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the visualizing amino acid sequences method of Beaver and Timlin to the methods by Jehl because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for visualizing amino acid sequences.
D. Claim 53 is rejected under 35 U.S.C. 103(a) as being unpatentable over Beaver in view of Elmqvist ("Rolling the dice: Multidimensional visual exploration using scatterplot matrix navigation." IEEE transactions on Visualization and Computer Graphics 14(6):1141-1148 (2008)), as cited on the attached Form PTO-892.
Claim 53 recites:
generating a dynamic amino acid sequence filter element including at least one movable bounding indicator, wherein the dynamic filter element visually represents an amino acid sequence range of a given target protein, and wherein the at least one movable bounding indicator visually represents a particular amino acid within the amino acid sequence range; and
visually distinguishing an amino acid sequence area of interest within the dynamic amino acid sequence filter element based on a position of the at least one movable bounding indicator on the dynamic amino acid sequence filter element corresponding to the particular amino acid
• Beaver teaches EpitopeViewer - a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules) (i.e. visualization of elements related to the amino acid sequence area of interest) (pg. 1 Abstract).
• Beaver does not teach "generating a dynamic … filter element including at least one movable bounding indicator, wherein the dynamic filter element visually represents a …range of a given target, and wherein the at least one movable bounding indicator visually represents a particular data point." However, Elmqvist teaches that the filtering mechanism called query sculpting allows for selecting data items in the main scatterplot visualization using 2D bounding volumes (boxes or convex hulls) and then iteratively refining the selection from other viewpoints while navigating the scatterplot matrix (pg. 1145 col. 1 para. 4)
• Beaver does not teach "visually distinguishing an … area of interest within the dynamic amino acid sequence filter element based on a position of the at least one movable bounding indicator on the dynamic … filter element corresponding to a data point." However, Elmqvist teaches an interactive methods to explore multidimensional data using scatterplots for interactive navigation (i.e. interactive graphical user interface) in the multidimensional space (pg. 1141 Abstract); wherein high-dimensional filtering is a standard feature of information visualization systems through the use of dynamic queries that allow for direct manipulation of conjunctive filters (pg. 11434 col. 1 para. 3); wherein the system supports the integration of query and filtering operations as well as their feedback directly into the visualization via the selection and filtering in data space using visual queries including axis-filtering (pg. 11434 col. 1 para. 4).
Rationale for combining (MPEP §2142-2143)
Regarding claim 53, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Beaver in view of Elmqvist because all references disclose methods for visualizing amino acid sequences. The motivation would have been to apply dimensions in the navigation space that can be reordered, manually or automatically, to highlight salient correlations and differences among them (pg. 1141 Abstract Elmqvist).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the visualizing amino acid sequences method of Beaver to the methods by Elmqvist because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for visualizing amino acid sequences.
E. Claims 54-57 are rejected under 35 U.S.C. 103(a) as being unpatentable over Beaver and Elmqvist as applied to claim 53 above further in view of Jehl as cited on the attached Form PTO-892.
Claim 54 recites:
further comprising updating an antibody product listing within the graphical user interface responsive to a user input by excluding antibody products with at least one amino acid sequence range value outside the amino acid sequence area of interest
• Neither Beaver or Elmqvist teach the recitation above. However, Jehl teaches the visualization of the protein architecture showing key features of the protein: secondary structure, topology, globular domains, SLiMs and PTM sites (i.e. reading on a range of antibody products included in the antibody product listings) (pg. W14 col. 1 para. 1); wherein the sequence data section displays protein and alignment data with, upon user request, alignments being filtered to display paralogue or orthologue alignments as well as complete homologue alignments (i.e. updating an antibody product listing within the graphical user interface responsive to a user input by excluding antibody products with at least one amino acid sequence range value outside the amino acid sequence area of interest) (pg. W12 col. 2 para. 1).
Claim 55 recites:
wherein the at least one movable bounding indicator includes a slider visually positioned on an edge of the amino acid sequence area of interest, and wherein moving the slider from a first location to a second location indicates a change to a length of the amino acid sequence area of interest
• Neither Beaver or Elmqvist teach the recitation above. However, Jehl teaches the visualization of the protein architecture showing key features of the protein: secondary structure, topology, globular domains, SLiMs and PTM sites; wherein users can directly specify a range of residues, move a slider (i.e. i.e. slider visually positioned on an edge of the amino acid sequence area of interest) or ctrl + click on a feature to select a target area and the selected area can be used to resize or highlight the visualization (i.e. wherein moving the slider from a first location to a second location indicates a change to a length of the amino acid sequence area of interest) (pg. W14 col. 1 para. 1)
Claim 56 recites:
further comprising a dynamic picklist within the computer-implemented interactive graphical user interface, wherein the dynamic picklist includes one or more of a particular amino acid or an amino acid sequence range of the given target protein, and is responsive to a user input to select at least one of the particular amino acid or amino acid sequence range
• Beaver does not teach the recitation above. However, Elmqvist teaches an interactive methods to explore multidimensional data using scatterplots for interactive navigation in the multidimensional space (pg. 1141 Abstract); wherein high-dimensional filtering is a standard feature of information visualization systems through the use of dynamic queries that allow for direct manipulation of conjunctive filters (i.e. dynamic picklist within the computer-implemented interactive graphical user interface) (pg. 11434 col. 1 para. 3). Furthermore, Jehl teaches a browser-based visualization tool to display protein features from precomputed multiple sequence alignments; (pg. W11 Abstract); wherein users can directly specify a range of residues (i.e. responsive to a user input to select at least one of the particular amino acid or amino acid sequence range), move a slider or ctrl + click on a feature to select a target area and the selected area can be used to resize or highlight the visualization (pg. W14 col. 2 para. 1).
Claim 57 recites:
further comprising a numerical entry interface within the computer-implemented graphical user interface, wherein the numerical entry interface is responsive to a user input to manually enter one or more of a particular amino acid or an amino acid sequence range of the given target protein
• Neither Beaver or Elmqvist teach the recitation above. However, Jehl teaches a browser-based visualization tool to display protein features from precomputed multiple sequence alignments; (pg. W11 Abstract); wherein users can directly specify a range of residues(i.e. reading on identifying a numerical value corresponding to residue numerical identification), move a slider or ctrl + click on a feature to select a target area and the selected area can be used to resize or highlight the visualization (pg. W14 col. 2 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 54-57, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Beaver and Elmqvist in view of Jehl because all references disclose methods for visualizing amino acid sequences. The motivation would have been to allow users with limited bioinformatic skills to rapidly access data pertinent to their research via visualizations customized with user defined data (pg. W11 Abstract Jehl).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the visualizing amino acid sequences method of Beaver and Elmqvist to the methods by Jehl because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for visualizing amino acid sequences.
Conclusion
No claims are allowed.
Regarding 101 issues, claims 1-3, 5-7, 10-11, 13-14, 16-17, 19-20, 22 and 53-57 appear to be patent eligible due to no judicial exceptions being identified at Step 2A Prong 1.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCINI A FONSECA LOPEZ whose telephone number is (571)270-0899. The examiner can normally be reached Monday - Friday 8AM - 5PM ET.
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/F.F.L./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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