Ex Parte Shilov

Patent Trials and Appeals Board

Jun 3, 2019

13697707 - (D) (P.T.A.B. Jun. 3, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
13/697,707 12/28/2012 Ignat V. Shilov
67050 7590 06/05/2019
KASHA LAW LLC
14532 DufiefMill Road
North Potomac, MD 20878
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www .uspto.gov
ATTORNEY DOCKET NO. CONFIRMATION NO.
IP0694-US 7675
EXAMINER
BORIN, MICHAEL L
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
06/05/2019 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
JOHN.KASHA@KASHALA W.COM
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte IGNAT V. SHILOV
Appeal 2017-011343
Application 13/697,7071
Technology Center 1600
Before ERIC B. GRIMES, FRANCISCO C. PRATS, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
Opinion for the Board filed by Administrative Patent Judge TOWNSEND.
Opinion Concurring filed by Administrative Patent Judge PRATS.
TOWNSEND, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a system
for calculating and recalculating protein confidence values, which have been
rejected as directed to patent ineligible subject matter. Oral argument was
heard May 1, 2019. We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.
1 Appellant identifies the real party in interest as DH TECHNOLOGIES
DEVELOPMENT PTE. LTD. (Appeal Br. 1.)
Appeal 2017-011343
Application 13/697,707
STATEMENT OF THE CASE
"In proteomics analysis, a sample is proteolytically digested into
surrogate peptide analytes that are identified by tandem mass spectrometry
coupled with a database search." (Spec. ,-J 2.) "The identifications of these
surrogate peptide analytes are then used to infer the detection of their parent
proteins" by assigning peptide confidence values "based on a heuristic or a
database search," to the surrogate peptide, which values are then used to
calculate protein confidence values. (Id.)
The present invention is directed to a system that uses a method of
calculating protein confidence values in a proteomic analysis from a
comparison of data measured by the mass spectrometer with data from a
protein database for distinguishing or identifying proteins in a sample
analyzed by a mass spectrometer. (Supplemental Appeal Br. 1, Apr. 29,
2017.)
Claims 1, 3, and 4 are on appeal. 2 Claim 1 is representative and reads
as follows:
1. A system for calculating and recalculating protein
confidence values by recalculating peptide confidence values in
proteomic analysis in order to distinguish proteins found in a
sample from random or false positive results, comprising:
a protein database;
one or more mass spectrometers that perform a plurality
of scans of a sample that is proteolytically digested into
surrogate peptide analytes producing a plurality of spectra; and
a processor in communication with the protein database
and the one or more mass spectrometers that
2 Claims 10-20 are pending but have been withdrawn from consideration.
(Advisory Action 1.)
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a. obtains the plurality of spectra from the mass
spectrometer,
b. identifies a plurality of peptides from the plurality of
spectra,
c. searches the protein database for proteins matching
peptides from the plurality of peptides producing a set of
proteins and a corresponding set of peptides,
d. determines peptide confidence values for the set of
peptides, wherein a peptide confidence, Ci, of an ith
peptide of the set of peptides is a probability that the ith
peptide is identified from the plurality of spectra,
e. calculates a protein confidence value for each protein
in the set of proteins based on one or more peptide
confidence values of one or more corresponding peptides
from the set of peptides, wherein a protein confidence
value Pp is a probability calculated according to
Pp= I-II(l-Ci),
where II( 1-Ci) is the product of one or more
peptide confidence values,
f. selects a protein from the set of proteins with a largest
protein confidence value, saves the largest protein
confidence value for the protein, removes the protein
from the set of proteins, and removes one or more
peptides corresponding to the protein from the set of
peptides,
g. recalculates the protein confidence value, Pp, for each
protein in the set of proteins based on one or more
peptide posterior probability values of one or more
corresponding peptides from the set of peptides
according to
Pp= I-II(l-P(+ I B)i),
wherein a posterior probability of the i1h peptide,
P( + I B), of the set of peptides is calculated using
P(+ I B)=P(B I+). P(+)
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P(B)
where P(B I+) is the peptide confidence value of the ;th
peptide, Ci, P(B) is the marginal probability of observing
the peptide with a given confidence, and P( +) is the prior
probability of randomly selecting a true positive and
P( +) is calculated from all confidence values of peptides
currently in the set of peptides and all confidence values
of peptides removed from the set of peptides to account
for the effect of removing the one or more peptides
corresponding to the removed protein from the set of
peptides, and
h. repeats steps ( f)-(g) until all proteins are removed from
the set of proteins or until a protein confidence value of
the selected protein with a largest protein confidence
value is below a threshold of interest and identifies
proteins found in the sample as the proteins with the
saved largest protein confidence values.
(Appendix A filed with Supp. Appeal Br. on April 29, 2017 at i-iii.)
The following ground of rejection by the Examiner is before us on
review:
Claims 1, 3, and 43 under 35 U.S.C. § 101 as being directed to non-
statutory subject matter.
DISCUSSION
The Appeal
The Examiner finds that the claims are directed to a system that
comprises a processor with instructions to execute a computational method
that includes "using mathematical formulas to compute peptide probabilities
3 The Final Action indicates claims 1, 4, and 21. However, Appellant
indicates that the claims subject to this rejection are claims 1, 3, and 4,
which are the only claims on Appeal. (Appeal Br. 9)
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and to recalculate them into protein probabilities." (Final Action 3; Ans. 2.)
The Examiner explains that the method "describes the concept of gathering
and combining data" and employing "mathematical relationships to
manipulate existing information to generate additional information." (Id.)
The Examiner points out that the "additional element of the claimed system
other than the abstract idea per se is a mass-spectrometer and processor, i.e.,
a known analytical device with processor addressed at high level of
generality." (Ans. 2; Final Action 3.) The Examiner explains that "[t]he
claims do not recite inventive steps outside of data manipulation, or
improvements to the function of the computer itself' and that "[t]here are no
meaningful limitations in the claims ... that transform the judicial exception
into a patent-eligible application such that the claim amounts to significantly
more than the exception itself." (Final Action 3-4; Ans. 3.)
Regarding preemption, the Examiner, among other things, notes that
the absence of preemption does not demonstrate patent eligibility and thus
that showing alternative uses of the judicial exception outside of the scope of
the claims does not establish patent eligibility where the claims are deemed
only to disclose patent ineligible subject matter. (Ans. 4.)
Appellant argues that the Examiner's rejection fails on technical
grounds as well as substantive ones. In particular, Appellant argues that the
Examiner did not point with specificity to the limitation as claimed that is
the abstract idea and explain why courts have identified such a limitation as
abstract, that the Examiner did not address the limitations as a combination
in determining whether the claim as a whole recited eligible subject matter,
and did not explain why the inclusion of specific structural components of
the system did not render the claims patent eligible as a particular useful
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application. (Appeal Br. 12-14.) Appellant contends that the claim is
directed to a technological improvement over protein identification
techniques and is so specific that it does not preempt all uses and as such is
directed to patent eligible subject matter. (Appeal Br. 14-30; Reply Br. 10-
14.)
After briefing was completed, in response to the changed landscape of
analyzing patent eligibility at the PTO, Appellant presented two additional
briefs. The first supplemental Appeal Brief was filed on October 30, 2018
("Supp. Appeal Br. I"), and the second supplemental Appeal Brief was filed
January 17, 2019 ("Supp. Appeal Br. II").4 In the first of these briefs,
Appellant argued that the technological improvement is tied to the steps f-h
of claim 1 and that those steps are not well-understood, routine, conventional
activity, even if they are drawn to the judicial exception. (Supp. Appeal Br.
I.) In the second of these briefs, Appellant assumes arguendo that the
Examiner properly articulated that claim 1 recites a judicial exception
because it includes mathematical concepts. (Supp. Appeal Br. II at 5.)
However, Appellant argues, similarly to the original Appeal Brief, that claim
1 integrates the mathematical probability formulas into a practical
application of identifying proteins in a sample using a mass spectrometer
and a protein database. (Supp. Appeal Br. II at 5-8.)
4 Appellant's first supplemental Appeal Brief was filed in response to the
April 19, 2018 memorandum to the Patent Examining Corps regarding
Berkheimer v. HP, Inc. The second supplemental Appeal Brief was filed
shortly after the PTO issued the 2019 Revised Patent Subject Matter
Eligibility Guidance ("Guidance"), 84 Fed. Reg. 50-57 (January 7, 2019).
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We address the Examiner's patent ineligibility rejection below, not
against the prior guidance extant at the time Appellant filed its Appeal Brief,
Reply Brief and First Supplemental Appeal Brief, but in accordance with the
current Guidance.
Analysis
35 U.S.C. § 101 defines patent eligible subject matter. The Supreme
Court has carved out exceptions to what would otherwise appear to be
within the literal scope of§ 101. Alice Corp. Pty. Ltd. v. CLS Bank Int 'l,
573 U.S. 208,216 (2014). One of these exceptions are claims "directed to"
an abstract idea. Id. at 217. This appeal involves the abstract idea exception
to patent eligibility under section 101.
The Supreme Court has established a two-step framework for
"distinguishing patents that claim laws of nature, natural phenomena, and
abstract ideas from those that claim patent-eligible applications of those
concepts." Id. "First, we determine whether the claims at issue are directed
to" a patent-ineligible concept. Id. If so, "we consider the elements of each
claim both individually and 'as an ordered combination' to determine
whether the additional elements 'transform the nature of the claim' into a
patent-eligible application." Id. ( quoting Mayo Collaborative Servs. v.
Prometheus Labs., Inc., 566 U.S. 66, 78-79 (2012)).
STEP 2A, Prong One:
Under the Guidance, in determining what concept a claim is "directed
to" in step one of the Supreme Court's two-step framework, we first look to
whether the claim recites any judicial exceptions, such as a mathematical
concept. Guidance at 52, 54 (Step 2A, Prong One). As conceded by
Appellant, claim 1 recites the use of mathematical probability formulas for
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determining peptide confidence values and protein confidence values.
(Supp. Appeal Br. II at 5.) These are steps d, e, and g of claim 1.
There is no dispute that claim 1, in reciting these formulae, recites
mathematical concepts that are considered an abstract idea. See Guidance at
52 (citing, e.g., SAP America, Inc. v. InvestPic, LLC, 898 F.3d 1161, 1163
(Fed. Cir. 2018) (holding that claims to a "series of mathematical
calculations based on selected information" are directed to abstract ideas);
Digitech Image Techs., LLC v. Elecs.for Imaging, Inc., 758 F.3d 1344, 1350
(Fed. Cir. 2014) (holding that claims to a "process of organizing information
through mathematical correlations" are directed to an abstract idea);
Bancorp Servs., LLC v. Sun Life Assurance Co. of Can.(U.S.), 687 F.3d
1266, 1280 (Fed. Cir. 2012) (identifying the concept of"managing a stable
value protected life insurance policy by performing calculations and
manipulating the results" as an abstract idea).)
STEP 2A, Prong Two:
Having made that determination, under the Guidance, we next
examine whether there are additional elements beyond the recited
mathematical formulae that integrate them into a practical application.
Under the Guidance, this is referred to as the "Prong Two" inquiry under
"Step 2A." Guidance at 54-55. That is, under the Prong Two analysis we
look to whether the claim as a whole "appl[ies ], rel[ies] on, or use[ s] the
judicial exception in a manner that imposes a meaningful limit on the
judicial exception." Id.
In performing this analysis, we are mindful that "a claim is not patent
eligible merely because it applies an abstract idea in a narrow way." BSG
Tech LLC v. BuySeasons, Inc., 899 F.3d 1281, 1287 (Fed. Cir. 2018). Thus,
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for example, the Supreme Court in Parker v. Flook, 437 U.S. 584 (1978),
found the use of a novel mathematical algorithm in a process for adjusting
alarm limits, which limits signal inefficiency or danger when exceeded, in
catalytic conversion of hydrocarbons patent ineligible. Mayo, 566 U.S. at 80
(discussing Flook, 437 U.S. at 585-87). The process included "the steps of:
(1) measuring the current level of the variable, e.g., the temperature; (2)
using an apparently novel mathematical algorithm to calculate the current
alarm limits; and (3) adjusting the system to reflect the new alarm-limit
values." Id. Moreover, the Supreme Court has stated that "simply
implementing a mathematical principle on a physical machine, namely a
computer, was not a patentable application of that principle." Id. at 84
(citing Gottschalkv. Benson, 409 U.S. 63, 71 (1972).)
On the other hand, the Supreme Court in Diamond v. Diehr, 450 U.S.
175 (1981), found the overall physical and chemical process for molding
precision synthetic rubber "patent eligible because of the way the additional
steps of the process integrated the equation into the process as a whole." See
e.g., Mayo, 566 U.S. at 80 (discussing Diehr, 450 U.S. at 177-79);
Recognicorp, LLC v. Nintendo Co. Ltd., 855 F.3d 1322, 1326 (Fed. Cir.
2017) ("In confirming patentability, the Supreme Court focused not on the
presence of a mathematical formula but on the subject matter of the claims
as a whole. [Diehr, 450 U.S.] at 192"). The process included "installing
rubber in a press, closing the mold, constantly determining the temperature
of the mold, constantly recalculating the appropriate cure time through the
use of the formula and a digital computer, and automatically opening the
press at the proper time." Mayo, 566 U.S. at 80-81. The Court stated: "[A]
claim containing a mathematical formula" satisfies § 101 when it
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"implements or applies that formula in a structure or process which, when
considered as a whole, is performing a function which the patent laws were
designed to protect, (e.g., transforming or reducing an article to a different
state or thing)." Diehr, 450 U.S. at 192. Outside of the math, Diehr was
directed to a process that was directed to otherwise eligible subject matter,
an industrial process for the molding of rubber products. Id. at 192-93; see
Thales Visionix Inc. v. United States, 850 F.3d 1343, 1348 (Fed. Cir. 2017)
("In terms of the modem day Alice test, the Diehr claims were directed to an
improvement in the rubber curing process, not a mathematical formula.").
We first note that unlike Diehr, the claims are not directed to a
process. They are system claims. But as the Supreme Court indicated in
Alice, whether a device is "a tangible system (in§ 101 terms, a 'machine')"
is not dispositive. See 573 U.S. at 224. Resolving the§ 101 inquiry based
on such an argument "would make the determination of patent eligibility
'depend simply on the draftsman's art."' Id. (quoting Flook, 437 U.S. at
593). Here, the system is directed at carrying out a process of distinguishing
proteins in a sample.
However, unlike the process performed in Diehr, the process carried
out by the claimed system does not involve additional elements beyond the
recited mathematical formulae that use the formulae to transform or reduce
an article into a different state or thing. It is true that proteins are required to
be digested to peptides for the processor to be able to distinguish the proteins
in the sample, but that is not a part of the system or a processor step. The
process that is recited to be carried out by the processor is one that starts
after the proteins have been digested. The processor "obtains the plurality of
spectra" and "identifies a plurality of peptides from the plurality of spectra."
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Thus, any transformation occurs prior to the process carried out by the
processor of the system; the processor just employs the mathematical
formulae.
The Examiner found that the claims do not recite inventive steps
outside of data manipulation, or improvements to the function of the
computer itself. (Final Action 3-4; Ans. 3.) We agree.
We examine the additional elements of the claim beyond the recited
mathematical calculations to determine whether they integrate the exception
into a practical application. The claims require the system to include a
protein database, at least one mass spectrometer, and a processor in
communication with both the protein database and the mass spectrometer(s).
In Appellant's view, a claim is not directed to an abstract idea at step one of
Alice so long as it recites limitations that render it narrower than the abstract
idea, e.g. the data collected here and acted upon is mass spectra of
proteolytically digested peptides of a protein sample. (Supp. Appeal Br. II at
6.) That a mass spectrometer and a protein database are required by the
claims, which are not generic computers, certainly limits the use of the
abstract idea to a particular technological environment. However, our
reviewing court has held "consistently ... that claims are not saved from
abstraction merely because they recite components more specific than a
generic computer." BSG Tech, 899 F.3d at 1286-87 ("the recitation of a
database structure slightly more detailed than a generic database does not
save the asserted claims at step one.").
The mass spectrometer, here, is used in its conventional manner to
obtain spectra of a sample of digested proteins by which the peptides are
then identified. (See, e.g., Spec. ,-J 2; Appeal Br. 5-6 (noting that steps a-e of
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the claim is conventional activity in calculating protein confidence values);
Supp. Appeal Br. II at 6; accord Supp. Appeal Br. I (arguing only that steps
f-h of the claims are not well-understood, routine or conventional activity);
US2006/0030053 5 iJiJ3-5.) In addition, the protein database is used in its
conventional manner in proteomic analysis, that is, it is consulted to
determine a set of sample proteins to which the identified peptides belong.
(Id.) These physical components are directed to pre-solution activity that
generates data used in the calculation of peptide confidence values, protein
confidence values, and recalculated protein confidence values. Even though
they may be "integral" to the ultimate ability to identify the proteins in the
sample "because they provide the inputs to the confidence calculations made
with the mathematical probability formulas" (Supp. Appeal Br. II at 6-7;
Appeal Br. 6-7), this pre-solution activity simply limits the technological
environment in which the mathematical formulae are used. (Accord
Amendment filed Apr. 4, 2016 at 33-34 (explaining that the calculation that
takes place at step g does not require the use of the mass spectrometer or the
use of a protein database and that these instruments are used to provide the
inputs for the calculation of confidence values and the recalculations that
take place using Bayes law in step g.)) They are not improved by the
calculations, i.e., the calculations do not provide a technological
improvement of the mass spectrometer or the protein database.
"Flook stands for the proposition that the prohibition against patenting
abstract ideas cannot be circumvented by attempting to limit the use of [the
5 Seymour et al., US2006/0030053 Al, published Feb. 9, 2006. This
reference was cited by the Examiner during prosecution of this application.
See Non-Final Action, Dec.7.2015, at 6-7.
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idea] to a particular technological environment." Alice, 573 U.S. at 222-23
(quoting Bilski v. Kappas, 561 U.S. 593, 610-611 (2010) (internal quotation
marks omitted); see also In re Grams, 888 F.2d 835, 840 ("[t]he presence of
a physical step in the claim to derive data for the algorithm will not render
the claim statutory."). Unlike the case in Diehr, Appellant's claimed mass
spectrometer and protein database do not integrate the equation into a
process; they limit the technological environment in which the abstract idea
is used. (See Supp. Appeal Br. II at 5 ("In other words, claim 1 is directed to
a system for identifying proteins in a sample analyzed by a mass
spectrometer using a specific method of calculating protein and peptide
confidence values from a comparison of data measured by the mass
spectrometer with data from a protein database.").) That is, even though
proteins are transformed into peptides, that transformation takes place prior
to implementation of the abstract idea. The abstract idea is then simply used
to analyze the data without any effects on the process itself. Thus, the fact
that the claim requires a mass spectrometer and a protein database is not
sufficient to support finding a "practical application." These additional
elements do not use a judicial exception in conjunction with a particular
machine, or apply the judicial exception at all. (See Supp. Appeal Br. II at
6-8.) Rather, as Appellant's arguments emphasize, the mass spectrometer
and protein database provide inputs to the mathematical formula.
Furthermore, there is no assertion that Appellant's invention improves
the collection of data in the protein database, or improves the manner by
which the set of sample proteins in which the peptides may be found is
collected. The mathematical analysis of the data collected from the protein
database via the spectra information does not provide input back to the
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database and it does not change the contents of the database. (Id.; accord
Appeal Br. 8.) In sum, there is not a "technological" improvement.
Such is consistent with the fact that the problem facing the inventor
was not how to digest peptides in order to determine proteins within a
sample, nor how to better use a mass spectrometer to observe peptides
within a digested sample. Rather, as the Specification indicates the problem
was to address the potential for the prior art's "calculation of high (false
positive) protein confidence[] values" (Spec. ,i 29) when evaluating the data.
Thus, the focus of the claims is the improved mathematical analysis.
Appellant does not appear to dispute that, asserting that "[t]he patentable
technological improvement provided by claim 1 is a specific method of
calculating protein confidence values from peptide confidence values
obtained from mass spectrometry data." (Appeal Br. 14-15.)
That leaves us with the question of whether the processor, which
applies the judicial exception to effect the calculation steps, imposes a
meaningful limit on the judicial exception. Appellant does not assert that the
processor is anything more than a generic computer component. It is the law
that "simply, implementing a mathematical principle on a physical machine,
namely a computer, [i]s not a patentable application of that principle."
Mayo, 566 U.S. at 84 (discussing Gottschalkv. Benson, 409 U.S. at 71); see
also In re Downing, Appeal No. 2018-1795, slip op. 9-10, and n2 (Fed. Cir.
Dec. 7, 2018) (unpublished).
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Appellant has explained that the process carried out by the processor
achieves an improvement over steps a-e alone (Shilov Declaration6 ,i,i 29-
32, 36-42), which steps a-e are admitted to be the conventional system and
manner employed for calculating protein confidence values in proteomic
analyses (Shilov Declaration,i 14 ). That improvement is derived not just
from the use of Bayes law in step g, but through the addition of step f, prior
to implementation of Bayes law. (Id.) In step f, a protein with the largest
protein confidence value is removed from the set of proteins determined in
step c and one or more peptides corresponding to the protein from the set
determined in step c is removed and then in step g the protein confidence
value is recalculated based on Bayes law. (Id.) As the Specification
explains it, this inserts information "about the sample or about the
relationships across peptides" into the calculation of confidence values that
did not exist in the prior art calculation model. (Spec. ,i,i 29-30.)
Irrespective of the improvement to the resulting data analysis, step f is
a data gathering step, like steps a-c that the generic processor carries out.
Thus, it too is pre-solution activity; it simply narrows down the data upon
which Bayes law is applied. Determining values for variables used in
mathematical formula does not save a claim from abstraction. In re
Richman, 563 F.2d 1026, 1030 (1977) ("[N]otwithstanding that the
antecedent steps are novel and unobvious, they merely determine values for
the variables used in the mathematical formulae used in making the
calculations. [They] do not suffice to render the claimed methods,
6 Declaration of Ignat Shilov filed August 30, 2016. This was the second
Declaration of Mr. Shilov filed during prosecution of the Application on
appeal. (Appeal Br. 3.)
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considered as a whole, statutory subject matter.") ( cited with approval in
Flook, 437 U.S. at 595).
Thus, the additional elements recited in the claim, namely the mass
spectrometer, the protein database, and the processer, do not reflect an
improvement in the functioning of the processor, or an improvement to mass
spectrometers or protein databases, or otherwise integrate the exception into
a practical application. See Guidance at 55. For the foregoing reasons,
therefore, we do not agree with Appellant that the additional elements reflect
an improvement in the technical field.
Appellant argues that the improvement in the identification of proteins
in a sample is like the improvement in computer animation in McRO, Inc. v.
Bandai Namco Games Am. Inc., 837 F.3d 1299 (Fed. Cir. 2016) and
therefore the claim is not directed to a judicial application. (Appeal Br. 16-
17.) We do not agree. In McRO, "the claimed improvement [was] allowing
computers to produce 'accurate and realistic lip synchronization and facial
expressions in animated characters' that previously could only be produced
by human animators." 837 F.3d at 1314. "The claimed rules in McRO
transformed a traditionally subjective process performed by human artists
into a mathematically automated process executed on computers. Id. [ at
1313-16]." Fairwarning IP LLC v. Iatric Sys., Inc., 839 F.3d 1089, 1094
(Fed. Cir. 2016). In short, in McRO the patent claimed an improvement in
computer animation. The additional elements, here, do not solve a
technological problem in the proteomic analysis field, nor do they improve
upon the technological process of peptide digestion for proteomic analysis.
Rather it is the application of the specific mathematical calculation in step g
that results in improved identification of proteins in the sample, i.e. an
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improvement in data analysis. Thus, we find that claim 1 is directed
essentially to a method of calculating, using mathematical formulae.
Appellant further argues that claim 1 does not preempt the calculation
of protein confidence values (Appeal Br. 18) and the additional requirements
of the claim do not preempt the use of Bayes law (Supp. Appeal Br. II at 9-
10) and thus, the claims should be deemed directed to patent eligible subject
matter. We do not find this argument persuasive. Preemption is sufficient to
render a claim ineligible under § 101, but its absence does not require a
conclusion of patent eligibility, as noted by the Examiner (Final Action 4).
Athena Diagnostics, Inc. v. Mayo Collab. Servs., LLC, 915 F.3d 743, 752
(Fed. Cir. 2019) (citing Flook, 409 U.S. at 71-72 (holding claim involving
mathematical formula invalid under § 101 that did not preempt a
mathematical formula); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d
1371, 1379 (Fed. Cir. 2015); In re BRCAJ- & BRCA2-Based Hereditary
Cancer Test Patent Litig., 774 F.3d 755, 764 n.4 (Fed. Cir. 2014). As just
discussed, claim 1 is directed to an abstract idea because it recites only the
collection of data, using standard equipment in proteomics, and applying
mathematical equations to that data to analyze that data.
STEP 2B
We next tum to Step 2B to evaluate whether the claims provide an
inventive concept. Guidance at 54.
As noted above, the process carried out by the processor includes a set
of unconventional steps that results in an improvement over the prior art
proteomic analysis: namely steps f and g, which are repeated in step h. As
noted, it is this unconventional gathering and processing of the data, that
achieves a reduction in the false positive protein identification. (Shilov
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Declaration ,i,i 14, 29, 40-41.) As the Guidance indicates, such
unconventional data gathering in combination with a specifically recited
application of it can render a claim patent eligible under § 101 despite the
fact that the judicial exception is not considered to be integrated into a
practical application. Id. at 55 and n.39 ( citing Exergen Corp. v. Kaz USA,
Inc., 725 F. App'x 959,966 (Fed. Cir. 2018).) Thus, while we agree with
the Examiner that the claim is directed to data manipulation, the inventive
steps involved in gathering the data for use in the Bayes law calculation, i.e.
step f which narrows the data in a particular way and which new data set is
employed in the recalculation using Bayes law to determine protein
confidence values, under the Guidance is sufficient to render the claims at
issue patent eligible under 35 U.S.C. § 101. Compare with SAP, 898 F.3d at
1168-69 (
all of the claim details identified by InvestPic-including in the
claims that emerged from reexamination-fall into one or both
of two categories: they are themselves abstract; or there are no
factual allegations from which one could plausibly infer that
they are inventive. In these circumstances, judgment on the
pleadings that the claims recite no "inventive concept" is
proper.)
Thus, we reverse the Examiner's rejection of claims 1, 3, and 4 under
35 U.S.C. § 101 as being directed to non-statutory subject matter.
REVERSED
18
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte IGNAT V. SHILOV
Appeal 2017-011343
Application 13/697,707
Technology Center 1600
Before ERIC B. GRIMES, FRANCISCO C. PRATS, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
PRATS, Administrative Patent Judge, concurring.
I concur with my colleagues that the Examiner's rejection should be
reversed. In my view, however, the rejection should be reversed under
Revised Step 2A, Prong 2, of the 2019 Revised Patent Subject Matter
Eligibility Guidance, 84 Fed. Reg. 50 (January 7, 2019) ("Memorandum" or
"Office Guidance").
The Office Guidance provides that we proceed to the analysis under
Revised Step 2B only if, under the analysis under Revised Step 2A, a claim
(1) recites a judicial exception and (2) does not integrate that exception into
a practical application. See 84 Fed. Reg. at 54 ("When the exception is so
integrated [into a practical application under the analysis in Revised Step
2A, Prong 2], then the claim is not directed to a judicial exception (Step 2A:
NO) and is eligible. This concludes the eligibility analysis.").
Appeal 2017-011343
Application 13/697,707
I agree with my colleagues that, under Revised Step 2A, Prong 1,
steps d, e, and g of Appellants' claim 1 recite mathematical equations. I
find, however, that under Revised Step 2A, Prong 2, the system recited in
Appellants' claim 1 integrates the abstract ideas into a practical application
because claim 1 requires the system to include a specific machine, a mass
spectrometer, and the system is limited to analyzing protein spectra obtained
from that machine. See Claims App'x at i-iii.
Because, in my view, Appellants' claims integrate the abstract ideas
into a practical application, I would reverse the Examiner's rejection without
reaching Step 2B of the Office Guidance.
2