Ex Parte Kilpinen et al

Patent Trial and Appeal Board

Jul 20, 2018

12936931 (P.T.A.B. Jul. 20, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/936,931 10/08/2010
466 7590
YOUNG & THOMPSON
209 Madison Street
Suite 500
Alexandria, VA 22314
07/24/2018
UNITED ST A TES OF AMERICA
FIRST NAMED INVENTOR
Sarni Kilpinen
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.
3501-1146-1 8029
EXAMINER
HARWARD, SOREN T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
07/24/2018 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):
DocketingDept@young-thompson.com
yandtpair@firs ttofile. com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte SAMI KILPINEN, REIJA AUTIO, and MATTI SAARELA
Appeal2017-007883 1
Application 12/936,931
Technology Center 1600
Before ERIC B. GRIMES, FRANCISCO C. PRATS, and RYAN H. FLAX,
Administrative Patent Judges.
PRATS, Administrative Patent Judge.
DECISION ON APPEAL
This appeal under 35 U.S.C. § 134(a) involves claims to methods that
involve obtaining data sets from experiments in which biological samples
are contacted with microarrays. The Examiner rejected the claims as being
directed to subject matter ineligible for patenting, and for obviousness.
We have jurisdiction under 35 U.S.C. § 6(b)(l).
We affirm.
The following rejections are before us for review:
(1) Claims 16-24 and 29, under 35 U.S.C. § 101 as being directed to
subject matter ineligible for patenting (Ans. 2-3); and
1 Appellants state that the "real party in interest in this appeal is the assignee
Medisapiens Oy, Helsinki, Finland." Br. 2.
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Application 12/936,931
(2) Claims 16-24 and 29, under 35 U.S.C. § I03(a) as being obvious
over Conway2 and Sidorov3 (id. at 3; see also Final Act. 5-9 (setting forth
Examiner's obviousness rationale)).
Claim 16 is representative and reads as follows:
16. A method, comprising: performing the following
steps by a data processor:
obtaining data sets from measurements of properties of
biological samples made with several different versions of a
microarray, each data set originating from one microarray,
wherein each microarray comprises several spots, each spot
indicating a biological quantity selected from a group
consisting of gene expression, microRNA expression, protein
abundance, protein binding, carbohydrate level and small
molecule activity;
storing the obtained data sets, wherein the storing
comprises associating each data set with an indication of a
version of the microarray the data set originates from;
determining at least one first spot-specific distribution
parameter and at least one second spot-specific distribution
parameter for each spot, wherein the at least one first spot-
specific distribution parameter is determined for each version
(i) of the microarray and the at least one second spot-specific
distribution parameter is determined for a combination of one
or more of the versions of the microarray, wherein said
combination of the one or more the versions comprises at least
one version other than version (i);
determining a spot-specific correction element for each
version of the microarray based on the discrepancy between the
at least one first spot-specific distribution parameter and the at
least one second property-specific distribution parameter;
2 US 2006/0047697 Al (published Mar. 2, 2006).
3 I.A. Sidorov et al., Oligonucleotide microarray data distribution and
normalization, 146 INFORMATION SCIENCES 67-73 (2002).
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Application 12/936,931
correcting a spot's indicated biological quantity with the
spot-specific correction element for the version of the
microarray on which the spot's indicated biological quantity is
based, thereby producing the spot's corrected indicated
biological quantity; and
outputting the spot's corrected indicated biological
quantity to a physical memory and/or display.
Br. 15-16.
STANDARD OF REVIEW
As stated in In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992):
[T]he examiner bears the initial burden ... of presenting a
primafacie case ofunpatentability ....
After evidence or argument is submitted by the applicant
in response, patentability is determined on the totality of the
record, by a preponderance of evidence with due consideration
to persuasiveness of argument.
PA TENT ELIGIBILITY
The Examiner's Prima Facie Case
In determining that Appellants' claims are directed to subject matter
ineligible for patenting, the Examiner finds that the "claims as a whole,
considering all claim elements both individually and in combination, do not
amount to significantly more than an algorithm that corrects biological
property measurements from one or more microarrays .... " Ans. 2.
In particular, the Examiner contends, a "series of data processing steps
or algorithm is a court-established abstract idea, and further is similar to
other court-established abstract ideas such as mathematical operations and
procedures for organizing information." Id.
The Examiner finds that the non-abstract steps recited in the claims,
i.e. obtaining data sets from microarray measurement, storing the data sets,
and outputting corrected values for the data based on the claimed algorithm
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"are highly generic data-input and -output steps, and are ubiquitous to any
data processing algorithm. Hence, they constitute insignificant extrasolution
activity." Id.
In addition, the Examiner finds, "numerous references of record ( e.g.
Conway) establish that such steps are ubiquitous when implementing
microarray measurement correction algorithms using a generic computer,
and that using computers for this purpose was a well-understood, routine and
conventional practice in the art prior to the time of invention." Id. at 2-3.
Therefore, the Examiner reasons, "[ v ]iewed individually and in their
context within the claims as a whole, these additional non-abstract claim
elements do not provide meaningful limitations to transform the abstract
idea into a patent eligible application of the abstract idea such that the claims
amount to significantly more than the abstract idea itself." Id. at 3.
Analysis
"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." 35 U.S.C. § 101.
The Supreme Court has "long held that this provision contains an
important implicit exception: Laws of nature, natural phenomena, and
abstract ideas are not patentable." Alice Corp. Pty. Ltd. v. CLS Bank Intern.,
134 S. Ct. 2347, 2354 (2014).
Our reviewing court has summarized the Supreme Court's two-part
test for distinguishing between claims to patent-ineligible exceptions, and
claims to patent-eligible applications of those exceptions, as follows:
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Step one asks whether the claim is "directed to one of
[the] patent-ineligible concepts." [Alice, 134 S. Ct. at 2354]. If
the answer is no, the inquiry is over: the claim falls within the
ambit of § 101. If the answer is yes, the inquiry moves to step
two, which asks whether, considered both individually and as
an ordered combination, "the additional elements 'transform the
nature of the claim' into a patent-eligible application." Id.
( quoting Mayo [ Collaborative Services v. Prometheus Labs.,
Inc., 132 S. Ct. 1289, 1297 (2012)]).
Step two is described "as a search for an 'inventive
concept."' Id. (quoting Mayo, 132 S. Ct. at 1294). At step two,
more is required than "well-understood, routine, conventional
activity already engaged in by the scientific community," which
fails to transform the claim into "significantly more than a
patent upon the" ineligible concept itself. Mayo, 132 S. Ct. at
1298, 1294.
Rapid Litigation Mgmt. Ltd. v. CellzDirect, Inc., 827 F.3d 1042, 1047 (Fed.
Cir. 2016) (paragraphing added).
In the present case, Appellants do not persuade us that the
preponderance of the evidence fails to support the Examiner's conclusion
that representative claim 16 recites subject matter ineligible for patenting. In
particular, Appellants do not persuade us that the Examiner failed to show
sufficiently that Appellants' claim 16 is directed to an abstract idea, without
significantly more.
Appellants contend that, under Enfish, LLC v. Microsoft Corp., 822
F.3d 1327 (Fed. Cir. 2016), the method recited in claim 16 is eligible for
patenting because "it improves the functionality of a computer-assisted
measurement system. Specifically, the present invention removes or
reduces the limitations of the prior art that measurements made with
microarrays of different versions are not comparable with each other." Br.
7-8.
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As support for the assertion that claim 16' s process improves
computer functionality, Appellants direct us to claim 16's step in which first
and second spot-specific distribution parameters are determined, and the
subsequent step in which a spot-specific correction element is determined,
based on the discrepancy between those distribution parameters. Id. at 8.
Appellants note that the correction element is then used to correct the
biological quantity indicated from a microarray experiment. See id. at 8-9.
Determining the claimed spot-specific distribution parameters,
however, is merely ascertaining the result of performing a mathematical
function. See Spec. ,r 8 ( describing "an appropriate distribution parameter
... as average, mean, or the like"). And Appellants identify no error in the
Examiner's finding that the claimed step of determining a correction
element, based on the discrepancy between two such mathematical values,
as well as the claimed step of applying that correction element to gathered
data, are also entirely mathematical operations.
Appellants do not identify any persuasive evidence of record
supporting their assertion that performing the mathematical operations
recited in claim 16 improves computer functionality, or solves a problem in
the software arts. Unlike the claim held patent-eligible in Enfish, claim 16
does not require the claimed data processor to employ any specific data
structures or other features that might distinguish the data processor from a
conventional computer. See Enfish, 822 F.3d at 1339 (distinguishing "the
self-referential table recited in the claims on appeal[, which] is a specific
type of data structure designed to improve the way a computer stores and
retrieves data in memory" from "a situation where general-purpose computer
components are added post-hoc to a ... mathematical equation").
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To the contrary, claim 16 involves only data gathering ("obtaining
data sets", "storing the obtained data sets"), data manipulation (determining
first and second spot-specific distribution parameters, determining a
"correction element," using the correction element to correct data), and data
"outputting." Br. 15-16.
Claim 16, therefore, is similar to claims found ineligible for patenting
in cases like Parker v. Flook, 437 U.S. 584 (1978) and Electric Power
Group, LLC v. Alstom S.A., 830 F.3d 1350 (Fed. Cir. 2016), which also
involved data gathering, data manipulation, and outputting data based on the
manipulation. See Parker, 437 U.S. at 585 (explaining that the process at
issue included three basic steps: "an initial step which merely measures the
present value of the process variable (e.g., the temperature); an intermediate
step which uses an algorithm to calculate an updated alarm-limit value; and
a final step in which the actual alarm limit is adjusted to the updated value")
(citations omitted); see also Electric Power Group, 830 F.3d at 1351-52
( claim at issue involved collecting and receiving data, analyzing the data to
determine whether there was a potential deficiency in the underlying system
(the power grid), and displaying (i.e., informing a user of) the analysis
results).
Appellants argue "the§ 101 rejection can be addressed by carrying
over arguments related to the§ 103 rejection." Br. 9. There is ample case
law support for the proposition that patent-eligibility and patentability ( e.g.,
over prior art) are separate issues and their analyses should not be mingled
(see, e.g., Diamond v. Diehr, 450 U.S. 175, 177 (1981)); however, as to
Appellants' contention (Br. 9-10) that Conway and Sidorov fail to suggest
the process recited in claim 16, as discussed below, we are not persuaded
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that Appellants have demonstrated error in the Examiner's conclusion of
obviousness and that any alleged error determines the outstanding question
of patent-eligibility. The fact that the process recited in claim 16 might be
novel and unobvious does not demonstrate its eligibility for patenting. See,
e.g., In re BRCAJ- and BRCA2-Based Hereditary Cancer Test Patent
Litigation, 774 F.3d 755, 759 (Fed. Cir. 2014) (Even if Appellants "made a
'[g]roundbreaking, innovative, or even brilliant discovery,' ... that is not
enough" to establish patent eligibility.) ( citing Association for Molecular
Pathology v. Myriad Genetics, Inc., 133 S.Ct. 2107, 2117 (2013)).
In sum, for the reasons discussed, Appellants do not persuade us that
the preponderance of the evidence fails to support the Examiner's
conclusion that representative claim 16 recites subject matter ineligible for
patenting. We, therefore, affirm the Examiner's rejection of claim 16 on that
ground. Claims 17-24 and 29 fall with claim 16. See 37 C.F.R.
§ 4I.37(c)(l)(iv).
OBVIOUSNESS
The Examiner's Prima Facie Case
In rejecting claims 16-24 and 29 over Conway and Sidorov, the
Examiner determined that Conway described a process having steps
corresponding to each of the steps recited in representative claim 16,
including the steps "c---e" of "normalizing (i.e. correcting) the data sets of
two different plates (0135) using one of several possible normalization
procedures, including global normalization (0140--0142)." Final Act. 6.
The Examiner conceded, however, that Conway differed from claim
16, in that "[ n Jone of the normalization procedures disclosed by Conway
teach the procedure recited in claim [16's] steps c---e," which recite the steps
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of determining first and second spot-specific distribution parameters,
determining a spot-specific correction element based on the discrepancy
between the first and second spot-specific distribution parameters, and
correcting a spot's indicated biological quantity using the spot-specific
correction element. Id.
As evidence that the process recited in representative claim 16 would
nonetheless have been obvious to an ordinary artisan, the Examiner cited
Sidorov as disclosing "a nonparametric normalization ( or histogram
normalization) procedure for microarray data (p. 70 § 4; see also p. 70 § 3
for introduction to normalization)." Id.
The Examiner found that Sidorov described calculating values for
intervals of a probe intensity histogram of an "array N to be normalized;
these constitute 'first spot-specific distribution parameter[ s] ... for each
version i of the microarray' (in the context of data analysis, the 'spot' of
Conway is equivalent to the 'probe' of Sidorov; cf Conway ,r 0005)" and
also calculating values for "a model reference array M; these constitute
'second spot-specific distribution parameter[s] ... for a combination of one or
more of the versions of the microarray, wherein said combination of the one
or more the versions comprises at least one version other than version i." Id.
at 7.
As to claim 16's steps of determining a spot-specific correction
element based on the discrepancy between the first and second spot-specific
distribution parameters, and using that element to correct a spot's indicated
biological quantity, the Examiner found that Sidorov disclosed that
"[p ]arameters a and b are then determined for each interval of array N
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( claimed step d), and these parameters are used to transform the probe
intensities ... of array N ( claimed step e ). " Id.
Id.
The Examiner further found:
Sidorov teaches that "both, parametric and nonparametric
normalization procedures, were better compared to the standard
global normalization approach" (p. 71 § 6), and that the
nonparametric approach was the best of the two (Abstract).
Furthermore, the nonparametric normalization procedure is a
generalization of global normalization (final ,r of p. 72).
Based on the references' combined teachings, the Examiner
determined that an ordinary artisan would have been "motivated to modify
the microarray data processing system of Conway to use the histogram
normalization procedure of Sidorov, because Sidorov teaches that the
nonparametric/histogram normalization procedure gives better normalization
than the standard global normalization procedure taught by Conway." Id. at
8.
The Examiner further reasoned that, "[g]iven that Sidorov teaches that
the nonparametric normalization is a generalization of, and simple substitute
for, the global normalization procedure taught by Conway, said practitioner
would have readily predicted that the modification would successfully result
in a microarray data processing system that uses nonparametric
normalization for the array data." Id. at 8-9.
Analysis
Appellants do not persuade us that the preponderance of the evidence
fails to support the Examiner's conclusion that the process recited in claim
16 would have been obvious to an ordinary artisan.
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Appellants contend that Conway and/or Sidorov do not teach or
suggest claim 16's step of determining first and second spot-specific
distribution parameters. Br. 11-13 (citing Conway ,r,r 77 and 78).
Specifically, Appellants contend, as "understood by a person of ordinary
skill in the art, the cited references disclose correction elements for oligo
spots, each of which is an individual or unique species and not a version, i.e.
genus of microarrays." Id. at 12. Further, Appellants argue that because
Conway and/or Sidorov do not teach or suggest claim 16's step of
determining first and second spot-specific distribution parameters, the
references necessarily cannot teach or suggest claim 16's steps of
determining a spot-specific correction element based on the discrepancy
between the first and second spot-specific distribution parameters, and
correcting a spot's indicated biological quantity using the spot-specific
correction element. Id. at 13-14.
We are not persuaded. We first note that Appellants concede that the
teachings in ,r,r 77 and 78 of Conway involve issues relating to different
microarray versions. See id. at 13. Appellants' arguments, moreover, do not
address the rejection as presented by the Examiner.
That is, even if it were true that ,r,r 77 and 78 of Conway did not teach
or suggest generating and using a spot-specific correction element as recited
by Appellants' claim 16, that fact does not address, much less demonstrate
error in, the Examiner's finding that other portions of Conway teach
normalizing the data sets of two different array versions. See Final Act. 6
(citing Conway ,r,r 135, 140-142).
We note, in addition, that the Examiner relied on Conway in
combination with Sidorov, as discussed above. It is well-settled that "[ n Jon-
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obviousness cannot be established by attacking references individually
where the rejection is based upon the teachings of a combination of
references. . . . [The reference] must be read, not in isolation, but for what it
fairly teaches in combination with the prior art as a whole." In re Merck &
Co., Inc., 800 F.2d 1091, 1097 (Fed. Cir. 1986).
Appellants do not specifically address, allege error in, or rebut by way
of a reply brief, the Examiner's finding that Sidorov teaches not only claim
16's step of determining first and second spot-specific distribution
parameters, but also the generation and use of a spot-specific correction
element as recited in claim 16, as well as the desirability of using Sidorov's
calculation method in Conway's across-version normalization procedure.
See Final Act. 6-9 (citing Sidorov 70-72); see also Ans. 6-8 (responding to
Appellants' arguments and explaining why the combination of Conway and
Sidorov suggests claim 16's process).
Because Appellants do not explain specifically why the Examiner's
characterization and interpretation of the particular cited portions of Conway
and Sidorov are erroneous, Appellants do not persuade us that the Examiner
failed to show, by a preponderance of the evidence, that the process recited
in representative claim 16 would have been obvious to an ordinary artisan.
We, therefore, affirm the Examiner's rejection of claim 16 over of Conway
and Sidorov. Claims 17-24 and 29 fall with claim 16. See 37 C.F.R.
§ 4I.37(c)(l)(iv).
SUMMARY
For the reasons discussed, we affirm both of the Examiner's
rejections.
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TIME PERIOD
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).
AFFIRMED
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