CosmosID Inc.

Patent Trials and Appeals Board

Feb 19, 2020

13836139 - (D) (P.T.A.B. Feb. 19, 2020)

UNITED STATES PATENT AND TRADEMARK OFFICE
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
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
13/836,139 03/15/2013 Nur A. HASAN 023658-0428709 5088
909 7590 02/19/2020
Pillsbury Winthrop Shaw Pittman, LLP
PO Box 10500
McLean, VA 22102
EXAMINER
ZEMAN, MARY K
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
02/19/2020 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):
docket_ip@pillsburylaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte NUR A. HASAN, TOM CEBULA, BOYD THOMAS
LIVINGSTON, HUAI LI, DAVID JAKUPCIAK, RITA R. COLWELL, and
DOUGLAS M. BRENNER
__________

Appeal 2019-002682
Application 13/836,1391
Technology Center 1600
__________

Before DONALD E. ADAMS, JOHN G. NEW, and
RACHEL H. TOWNSEND, Administrative Patent Judges.

TOWNSEND, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a
computer implemented system for characterizing an organism in a sample,
which have been rejected as being directed to patent-ineligible subject
matter. Oral argument was heard on February 3, 2020. We have jurisdiction
under 35 U.S.C. § 6(b).
We affirm.

1 We use the word “Appellant” to refer to “Applicant” as defined in 37
C.F.R. § 1.42. Appellant identifies the real party in interest as CosmosID
Inc. (Appeal Br. 2.)
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STATEMENT OF THE CASE
Claims 78–83 are on appeal. Claim 78 is representative and reads as
follows:
78. A computer implemented system for characterizing an
organism in a sample, the system comprising:
one or more processors programmed with computer
program instructions that, when executed, cause the system to,
(a) receive sample sequence information
comprising over 1000 unassembled nucleotide fragment
reads derived from an organism in a sample;
(b) identify each occurrence of a predefined anchor
sequence of 2 to 8 base pairs in length within the reads
derived from the organism;
(c) for each occurrence of the anchor sequence
identified in (b), generate a sample-derived n-mer of 9 to
20 nucleotides in length where the n-mer is a nucleic acid
sequence adjacent to the occurrence of the anchor
sequence within the reads derived from the organism in
the sample, thereby providing a plurality of sample-
derived n-mers;
(d) receive trait-specific reference sequence
information comprising trait-specific nucleotide
sequences derived from thousands of microbial genomes
wherein each trait-specific nucleotide sequence is
associated with a phenotypical trait, the phenotypical trait
being at least one of a virulence factor, an antibiotic
resistance trait, a pathogenicity trait, a bioterror agent
marker, or a biochemical trait;
(e) identify each occurrence of the anchor
sequence within the trait-specific nucleotide sequences;
(f) for each occurrence of the anchor sequence
identified in (e), generate a trait-specific n-mer of 9 to 20
nucleotides in length where the trait-specific n-mer is a
nucleic acid sequence adjacent to the occurrence of the
anchor sequence within the trait-specific nucleotide
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sequences, thereby providing a plurality of trait-specific
n-mers;
(g) determine an amount of the sample-derived n-
mers that match one or more trait-specific n-mers that are
associated with a same phenotypical trait; and
(h) determine, based on the amount determined in
(g), the presence of one or more of the phenotypical traits
in the organism in the sample.
(Appeal Br. 20.)

The following ground of rejection by the Examiner is before us on
review:
Claims 78–83 under 35 U.S.C. § 101 as being directed to patent-
ineligible subject matter.
DISCUSSION
The Dispute
The Examiner finds that claim 78 is “directed to characterizing
organisms based on sequence information which is matched to trait data”
using a general purpose computer. (Final Action 2–3.) The Examiner finds
that “the steps” the general purpose computer uses are:
[Claim 78 (a)] Get sequence information (gather data);
[Claim 78 (b)] Identify each occurrence of a predefined
“anchor” sequence (mental step/comparison);
[Claim 78 (c)] Generate/select a subset of sequences from the
original sequence information (selecting is another mental
step— nothing is actually generated);
[Claim 78 (d)] Receive reference sequence information (gather
data);
[Claim 78 (e)] Identify occurrences of the anchor sequence in
the reference data (mental step/comparison);
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[Claim 78 (f)] Generate/select another subset of data (mental
step);
[Claim 78 (g)] Determine an amount (calculate); and
[Claim 78 (h)] Detect/identify presence of phenotypic trait
(mental step).
(Id. at 3 (formatting added for ease of reading).) The Examiner explains that
all of the steps are directed to abstract-idea categories identified by the
Federal Circuit and summarized in FairWarning IP, LLC v. Iatric Systems,
Inc., 839 F.3d 1089 (Fed. Cir. 2016), including
collecting information, including when limited to particular
content.’ (Electric Power (Fed. Cir. 2016) . . . “analyzing
information by steps people go through in their minds, or by
mathematical algorithms, without more, as essentially mental
processes within the abstract-idea category.” . . . [and] “merely
presenting the results of abstract processes of collecting and
analyzing information, without more (such as identifying a
particular tool for presentation), is abstract as an ancillary part
of such collection and analysis.”
(Id. at 4.) The Examiner notes:
Specifically, in the claims, steps a and d, the receipt of
organism specific sequence data, and trait specific reference
sequence data, are data collection, steps b-c, e-g are the analysis
of the data, including string matching and counting elements
which are performed through mathematical algorithms, and step
[h]2 merely presents the results without more.
(Id.) The Examiner further explains that the claim is not focused on “an
improvement in computers as tools, but on certain independently abstract
ideas that use computers as tools.” (Id. at 5.) The Examiner further finds

2 While the Examiner identified step d here, we believe the Examiner meant
step h, as step d was already mentioned as being a data collection step of
receiving trait-specific sequence data and the Examiner did not otherwise
refer to step h.
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that “string matching and counting are routine, well understood and
conventional steps in sequence analysis and language processing analysis”
and thus the claim does not require “unusual steps previously unable to be
performed.” (Id. at 4–5.) The Examiner also explains that “[c]omparison of
sequence data with a reference set of data, counting any matches, and
drawing a conclusion are all routine, well understood and conventional steps
in bioinformatics.” (Id. at 5.)
In addition to the abstract idea analysis, the Examiner notes that the
claims include a natural law/principle, namely that an organisms naturally
occurring genetic sequence data is analyzed and the information about that
sequence data is correlated to a phenotypic trait of the organism. (Id.) The
Examiner explains that “[t]he instant claims inform the user of the natural
law that exists regarding aspects of an organism, a phenotypic trait. The
independent claims lack a practical application of the trait.” (Id. at 5–6.)
Finally, the Examiner determines that the elements in addition to the
abstract ideas and natural law are a nonspecific computer system including a
generic relational database (the n-mer sample sequence library database and
the trait-specific sequence library database), and receiving data. (Id. at 6.)
The Examiner finds that “the courts have explained, the use of generic
computer elements like a microprocessor or user interface do not alone
transform an otherwise abstract idea into patent-eligible subject matter. See
DDR Holdings (Fed. Cir. 2014).” (Id.)
The Examiner further finds that the generic relational databases do not
improve or change the way the computer functions and that matching
sequences in bioinformatics is not a problem rooted in computer technology
though it may be “impractical and tedious to analyze bioinformatics data
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without an electronic computer.” (Id. at 6–7.) The Examiner explains that
“[t]he abstract steps themselves do nothing to the actual structure of the
computer or the processors etc. These are program steps of analyzing and
selecting data. Nothing more.” (Id. at 10.) Thus, the Examiner concludes
that the claim does not include additional elements sufficient to amount to
significantly more than the judicial exceptions. (Id. at 6.)
Furthermore, the Examiner finds that the claim does “not require any
particular machines or physical elements being used in an unconventional
manner. The claims are all drawn to steps of collecting information, and/or
are equivalents of mental steps.” (Id. at 8–9.) And the Examiner finds that
the claims “do not provide any step where the abstract idea interacts with or
is applied to a particular machine” and “no improvement appears to be
effected on or by way of machinery.” (Id. at 9.) In short “[t]he claims
merely require standard computer elements in a normal arrangement to
perform the programmed process.” (Id. at 9–10.)
Appellant contends that the Examiner’s rejection is in error because
she failed to properly analyze the claims as a whole and thus did not
appreciate
[(1)] that the ordered combination of the claim limitations
enable embodiments of the claimed invention to “distinguish
pathogens [or other microorganisms] even between different
strains present in metagenomic data in just a few minutes.”
Specification at ¶ 144. . . .
[(2)] that it is the ordered combination of the claim limitations
that enable embodiments of the claimed invention to
significantly reduce computational resource usage and increase
the identification accuracy at the sub-species or strain level, as
compared to pre-existing whole genome-based methods.
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(Appeal Br. 9–10; Reply Br. 2–3.) Appellant argues that the claim elements
as an ordered combination provide an improvement to another technology or
technical field like the claims in Thales Visionix Inc. v. United States, 850
F.3d 1343 (Fed. Cir. 2017), Enfish LLC v. Microsoft Corp., 822 F.3d 1327
(Fed. Cir. 2016), and McRO, Inc. v. Bandai Namco Games America Inc.,
837 F.3d 1299 (Fed. Cir. 2016). (Id. at 6–7, 15–17; see also Reply Br. 14–
17.)
Furthermore, argues Appellant, even if the process steps individually
are abstract, the Examiner erred in not analyzing the claim limitations as an
ordered combination in determining whether the claim included an inventive
concept, such as a non-conventional and non-generic arrangement of
conventional pieces as in BASCOM Global Internet Services, Inc. v. AT&T
Mobility, 827 F.3d 1341 (Fed. Cir. 2016), and thus transformed the nature of
the claim into a patent eligible application. (Appeal Br. at 10–12, 14.)
According to Appellant, the claim’s “ordered combination as a whole
provides an improvement to another technology or technical field (e.g.,
metagenomics analysis methods/systems) by significantly reducing
computational resource usage and/or increasing the identification accuracy
at the subspecies or strain level.” (Appeal Br. 13.) Appellant further notes
that
in contrast to pre-existing metagenomics analysis
methods/systems, the claimed invention enables a
metagenomics analysis system to avoid the need to “first
assemble the fragment data into contiguous segments (contigs)
or whole genomes” (Specification at ¶ 165). Moreover, unlike
pre-existing metagenomics analysis methods/systems, short
fragment reads (e.g., as short as 12 to 50 base pairs) from a
sample may still be useful to determine the presence of
phenotypic traits in organisms in the sample because the
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claimed invention utilizes the combination of anchor sequences
of 2-8 base pairs in length and short n-mers of 9-20 nucleotides
in length to perform such determination.
(Id. at 14–15.)
We address independent claim 78, as Appellant has not argued claims
79–83 separately.
The Analysis
35 U.S.C. § 101 defines patent-eligible subject matter. An invention
is patent-eligible if it claims a “new and useful process, machine,
manufacture, or composition of matter.” 35 U.S.C. § 101. The Supreme
Court, however, has carved out exceptions to what would otherwise appear
to be within the literal scope of § 101, e.g., claims to “[l]aws of nature,
natural phenomena, and abstract ideas.” Alice Corp. v. CLS Bank Int’l, 573
U.S. 208, 216 (2014).
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. at 217. “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)). “A claim that
recites an abstract idea must include ‘additional features’ to ensure ‘that the
[claim] is more than a drafting effort designed to monopolize the [abstract
idea].’” Id. at 221 (alterations in original) (quoting Mayo, 566 U.S. at 77).
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“[M]erely requir[ing] generic computer implementation[] fail[s] to transform
that abstract idea into a patent-eligible invention.” Id.
The United States Patent and Trademark Office (“PTO”) issued the
2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”),
indicating how the PTO would analyze patent eligibility under the Supreme
Court’s two-step framework. 84 Fed. Reg. 50–57 (January 7, 2019).
Appellant’s claim 78 recites: “A computer implemented system for
characterizing an organism in a sample. . . . .” Following the first step of the
eligibility analysis, id. at 53, we find that the claim, being a computer
(machine), falls into one of the four statutory categories of patent-eligible
subject matter identified by 35 U.S.C. § 101.
Under the Guidance, in determining what concept the claim is
“directed to,” we next look to whether the claim recites any judicial
exceptions, including laws of nature, natural phenomena, and/or abstract
ideas. Id. at 53–54 (“Step 2A, Prong One”). If it does, then we look to
whether the claim recites additional elements that integrate the recited
judicial exception into a practical application. Id. at 54–55 (citing MPEP
§ 2106.05(a)–(c), (e)–(h)) (“Step 2A, Prong Two”).
If a claim (1) recites a judicial exception and (2) does not integrate
that exception into a practical application, i.e., it is found to be “directed to”
a judicial exception, we then look to whether the claim contains an
“‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception
into a patent-eligible application of the judicial exception. Guidance, 84
Fed. Reg. at 56 (“Step 2B”); see also Alice, 573 U.S. at 221 (quoting Mayo,
566 U.S. at 82). Under Step 2B, we examine the claim to determine whether
it adds a specific limitation beyond the judicial exception that is not “well-
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understood, routine, conventional” in the field (see MPEP § 2106.05(d)); or
simply appends well-understood, routine, conventional activities previously
known to the industry, specified at a high level of generality, to the judicial
exception. Guidance, 84 Fed. Reg. at 52–56.
Applying the Guidance, we agree with the Examiner’s conclusion that
claim 78 is directed to patent-ineligible subject matter and does not include
additional features sufficient to transform the claimed abstract idea into a
patent-eligible application of the abstract idea.
STEP 2A, Prong One:
In Step 2A, Prong One of the Guidance, we evaluate whether claim 78
recites a judicial exception, such as “mental processes––concepts performed
in the human mind (including an observation, evaluation, judgement,
opinion).” Guidance, 84 Fed. Reg. at 52. In its Reply Brief, Appellant
argues that “the claims are patent-eligible because they ‘do not recite matter
that falls within [the] enumerated groupings of abstract ideas” in the
Guidance. (Reply Br. 2.) According to Appellant:
the independent claims do not recite any particular
mathematical relationship, mathematical formula/equation, or
mathematical calculation. The independent claims also do not
recite any fundamental economic principle or practice,
commercial or legal interaction, or management of personal
behavior or relationships or interactions between people. The
independent claims further do not recite any concept that is
performed in the human mind.
(Id. at 5.) During oral argument, Appellant’s counsel conceded that each
one of (b), (c), and (e)–(h) of claim 78 recited an abstract idea under the
Guidance, although not specifying which category of abstract idea.
We agree with the Examiner’s evaluation (Final Action 3) that there
are several mental steps recited in claim 78, and thus the claim recites
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judicial exceptions. First, steps (b) and (e) require instructions that cause the
system to “identify” an “anchor sequence” (predefined and being 2 to 8 base
pairs in length) within nucleotide sequence data sets (i.e., the received
fragment reads of step (a) and the received trait-specific reference sequences
of step (d)) that the system has been caused to receive by executing other
instructions. Such an identification may be made by observing whether any
particular reads include the anchor sequence, which is a mental step under
the Guidance. Although the data set from which the observation is made in
step b is “over 1000 unassembled nucleotide fragment reads” and admittedly
a large data set, the observation is still capable of being made by a human
albeit less quickly than a computer can. The same is true for the
identification to be made in the trait-specific reference sequence data set.
Second, we agree with the Examiner that the two steps (c) and (f) that
require instructions that cause the system to “generate” an n-mer of 9 to 20
nucleotides “where the n-mer is a nucleic acid sequence adjacent to the
occurrence of the anchor sequence” identified in (b) and (d) respectively is
simply an identification of a further subset of sequences from the two data
sets, or in the Examiner’s terms a “select[ion] of a subset of sequences from
the original sequence information.” (Final Action 3.) These steps, but for
the recitation of computer implementation, can be effected by a human
observing the additional n-mer sequences adjacent to the observed anchor
sequences in the sample reads and the trait specific sequence data set. Thus,
like (b) and (d), (c) and (f) are mental steps under the Guidance.
Step (g) requires instructions that cause the system to determine an
amount of matches between the sample derived n-mer data set and the trait-
specific n-mer data set “that are associated with a same phenotypical trait.”
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This too is a mental step involving observation that can be performed by a
human, i.e., a mental step; that is the two data sets are compared, and
matches are counted.
Step (h) requires instructions that determine the presence of a
phenotypical trait in the sample based on the amount of matches determined
in step (g). This step simply requires that one make a mental connection
between the matched n-mer of the sample to the phenotypical trait associated
with the trait-specific nucleotide sequence to which it was matched. Thus,
steps (g) and (h) are also mental steps under the Guidance.
We address the issue of practical application under STEP 2A, Prong
Two of the Guidance, below. Guidance, 84 Fed. Reg. at 54–55.
STEP 2A, Prong Two:
In the Prong Two analysis, we examine whether there are additional
elements beyond the judicial exception that integrate it into a practical
application. Id. (integration into a practical application is evaluated by: “(a)
Identifying whether there are any additional elements recited in the claim
beyond the judicial exception(s); and (b) evaluating those additional
elements individually and in combination to determine whether they
integrate the exception into a practical application, using one or more of the
considerations laid out by the Supreme Court and the Federal Circuit.”).
That is we look to the claim to see if it “appl[ies], rel[ies] on, or use[s] the
judicial exception in a manner that imposes a meaningful limit on the
judicial exception.” Id. at 53.
Appellant contends that there is integration “at least because the
claimed inventions provide a technical solution to one or more problems of
pre-existing metagenomics analysis methods/systems.” (Reply Br. 5.)
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However, Appellant does not identify the steps or elements of the claim that
are additional to the abstract ideas in explaining the alleged technical
solution. Rather, Appellant indicates that the combination of the mental
steps discussed above is what achieves “a significant reduction in
computational resource usage and also avoiding the use of error-prone
assembled contiguous segments of whole genomes.” (Id. at 6.) In
particular, Appellant states:
To address the foregoing issues of the pre-existing
metagenomics analysis methods/systems, the claimed invention
involves a computer-implemented system configured to (i)
identify anchor sequences respectively in sample-derived
unassembled nucleotide fragment reads and trait-specific
reference nucleotide sequences, (ii) generate short sample-
derived n-mers (e.g., of 9-20 nucleotides in length) and short
trait-specific n-mers (e.g., of 9-20 nucleotides in length) based
on the respective anchor sequences, and (iii) identify matches
between the short sample-derived n-mers and the short trait-
specific n-mers to determine the presence of one or more
phenotypic traits in organisms in a sample. Such use of
predefined anchor sequences and the short n-mers of 9-20
nucleotides in length (in the manner specifically recited in the
claims) “distinguish pathogens [or other microorganisms] even
between different strains present in metagenomic data in just a
few minutes.” Specification at ¶ 144.
(Id. (emphasis in the original); see also Appeal Br. 7–8.) We do not find
Appellant’s argument persuasive. “An inventive concept that transforms the
abstract idea into a patent-eligible invention must be significantly more than
the abstract idea itself.” BASCOM, 827 F.3d at 1349.
There are two steps of claim 78 that we did not consider to recite an
abstract concept as provided in the Guidance. Those steps, however, are
data gathering steps. At step (a), the program instructions cause the
computer processor to automatically receive the nucleotide read data from
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an organism, and at step (d), the program instructions cause the computer
processor to automatically receive the trait-specific reference sequence
information. Neither of these data gathering steps applies, relies on, or uses
the mental process steps discussed above. Rather, the mental process steps
avail themselves of the data gathered in steps (a) and (d). The data gathering
in steps (a) and (d) constitutes insignificant pre-solution activity. See MPEP
§ 2106.05(g):
An example of pre-solution activity is a step of gathering data
for use in a claimed process, e.g., a step of obtaining
information about credit card transactions, which is recited as
part of a claimed process of analyzing and manipulating the
gathered information by a series of steps in order to detect
whether the transactions were fraudulent.
See also CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1372
(Fed. Cir. 2011) (“[E]ven if some physical steps are required to obtain
information from the database . . . such data-gathering steps cannot alone
confer patentability.”).
In addition to the “steps” the system is caused to perform through
executed computer program instructions, claim 78 requires the system to
include “one or more processors.” The processor is recited generically as
simply a “processor” and the activity performed by that generic processor is
normal computer functionality, i.e., receive information, storing that
information, and comparing information. The requirement of using a
computer processor is not sufficient to establish integration of the abstract
idea into a practical application. One of the “examples in which a judicial
exception has not been integrated into a practical application” is when “[a]n
additional element . . . merely includes instructions to implement an abstract
idea on a computer, or merely uses a computer as a tool to perform an
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abstract idea.” Guidance 84 Fed. Reg. at 55 (emphasis added);
FairWarning, 839 F.3d at 1096 (“[T]he use of generic computer elements
like a microprocessor or user interface do not alone transform an otherwise
abstract idea into patent-eligible subject matter.”) (Citation omitted.).
That the claimed system may result in faster and more accurate
identifications in large data sets does not take the claim out of the realm of
the abstract. “[R]elying on a computer to perform routine tasks more
quickly or more accurately is insufficient to render a claim patent eligible.”
OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363 (Fed. Cir. 2015);
see also Intellectual Ventures I LLC v. Erie Indemnity Co., 711 F. App’x
1012, 1017 (Fed. Cir. 2017) (unpublished) (“Though the claims purport to
accelerate the process of finding errant files and to reduce error, we have
held that speed and accuracy increases stemming from the ordinary
capabilities of a general-purpose computer ‘do[ ] not materially alter the
patent eligibility of the claimed subject matter.”’); see also Bancorp Servs.,
L.L.C. v. Sun Life Assurance Co. of Can. (U.S.), 687 F.3d 1266, 1278 (Fed.
Cir. 2012) (“[T]he fact that the required calculations could be performed
more efficiently via a computer does not materially alter the patent eligibility
of the claimed subject matter.”).
Whether examined individually or in combination, the additional
elements of the claim beyond the mental steps, i.e., data collection and
computer implementation, are insufficient to establish that the abstract ideas
recited are integrated into a practical application. Appellant’s additional
elements recited in claim 78, considered individually and as an ordered
combination, do not (1) improve the functioning of a computer or other
technology, (2) are not applied with any particular machine (except for
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generic computer parts), (3) do not effect a transformation of a particular
article to a different state, and (4) are not applied in any 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. See MPEP
§ 2106.05(a)–(c), (e)–(h).
We do not find persuasive Appellant’s arguments that the claimed
system is patent-eligible like the claims in McRO, Enfish, Thales, and
BASCOM.
In McRO, it was not the mere presence of unconventional rules that
led to patent eligibility. In McRO, “[t]he claimed improvement was to how
the physical display operated (to produce better quality images).” SAP Am.
v. InvestPic, LLC, 898 F.3d 1161, 1167 (Fed. Cir. 2018). The claims in
McRO recited a step of applying the data sets generated using the specific
claimed rules to a sequence of animated characters to produce lip
synchronization and facial expression control of those animated characters.
McRO, 837 F.3d at 1308. Thus, the claims were directed to an improvement
in computer animation and used rules to automate a subjective task of
humans to create a sequence of synchronized, animated characters. Id. at
1314–15. In the claims at issue here, there is no such application of
specifically claimed rules to produce an improved technological result. The
process of characterizing what phenotypical traits are present in an unknown
sample based on finding out the sequence information in that sample is not a
technological process; it is information evaluation.
The disputed claims in Enfish were patent-eligible because they were
“directed to a specific improvement to the way computers operate, embodied
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in [a] self-referential table.” Enfish, 822 F.3d at 1336. The court found that
the “plain focus of the claims” there was on an improvement to computer
functionality itself—a self-referential table for a computer database,
designed to improve the way a computer carries out its basic functions of
storing and retrieving data— not on a task for which a computer is used in
its ordinary capacity. Id. at 1335–36. For example, a representative claim
recited a data storage and retrieval system for a computer memory having a
means for configuring a memory according to a logical table that included
rows, columns, and a means for indexing data. Id. at 1336. The means for
configuring required a four-step algorithm, and the third step of that
algorithm (i.e., “[f]or each column, store information about the column in
one or more rows”), rendered the table self-referential. Id. The court noted
that the specification identified additional benefits conferred by the self-
referential table (e.g., increased flexibility, faster search times, and smaller
memory requirements), which further supported the court’s conclusion that
the claims were directed to an improvement of an existing technology. Id. at
1337 (citation omitted).
Here, in contrast, Appellant does not purport to have invented a data
structure analogous to Enfish’s self-referential table. And Appellant fails to
explain sufficiently and persuasively how claim 78 is directed to an
improvement in the way computers operate analogous to the case in Enfish.
We find instead that Appellant’s claim merely uses generic computer
components (e.g., a processor and memory) that operate in their normal,
expected manner.
Appellant’s reliance on Thales, is likewise unavailing. In Thales, the
court held patent-eligible claims reciting determining an orientation of an
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object relative to a moving reference frame based on signals from two
inertial sensors mounted respectively on the object and on the moving
reference frame. Thales Visionix, 850 F.3d at 1345–49. In reaching its
eligibility conclusion, the court noted that the claimed invention used inertial
sensors in an unconventional manner to reduce errors in measuring a moving
object’s relative position and orientation on a moving reference frame. Id. at
1348–49. In other words, the court relied on the particular arrangement of
sensors, not the mathematical equations, as the improvement in finding
claims eligible.
Similarly, in BASCOM, the claims recited a “specific method of
filtering Internet content” requiring “the installation of a filtering tool at a
specific location, remote from the end-users, with customizable filtering
features specific to each end user.” BASCOM, 827 F.3d at 1345–46, 1350.
The installation of a filtering tool at a specific location, remote from the end
users, with customizable filtering features specific to each end user,
provided an inventive concept in that it gave the filtering tool both the
benefits of a filter on a local computer and the benefits of a filter on the ISP
server. Id. at 1350.
Appellant fails to explain sufficiently and persuasively how claim 78
is analogous to these cases. We find no analogous non-conventional, non-
generic arrangement of known, conventional physical elements within a
computer system. That is the claim does not recite any physical element
positioned in an unconventional manner in the system.
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While the “rules” recited in the claim3 (1) serve to identify certain
sequence information in the sample and reference data received by the
processor and the computer (2) may speed up the time it takes to analyze the
collected data so as to determine what phenotypic traits as represented by a
particular nucleotide sequence may be present in the sample and (3) avoid
assembly of contiguous sequences or whole genomes, those rules are the
abstract idea and they do not improve computer technology per se or provide
an improved technological result. The claim instead invokes computers in
the collection of data and analysis of data. Claims that recite performing
information analysis (e.g., statistical analyses and correlating ontological
information), as well as the collection and manipulation of information
related to such analysis, have been determined by our reviewing court to be
an abstract concept that is not patent eligible. See SAP, 898 F.3d, 1165,
1167, 1168 (Claims reciting “[a] method for providing statistical analysis”
(id. at 1165) were determined to be “directed to an abstract idea” (id. at
1168)); see also Content Extraction & Transmission LLC v. Wells Fargo
Bank, Nat’l Ass’n, 776 F.3d 1343, 1345, 1347 (Fed. Cir. 2014) (finding the
“claims generally recite . . . extracting data . . . [and] recognizing specific
information from the extracted data” and that the “claims are drawn to the
basic concept of data recognition”).
“As many cases make clear, even if a process of collecting and
analyzing information is limited to particular content or a particular source,

3 Those rules are (1) that the anchor sequence to be identified is from 2 to 8
based pairs in length and (2) the n-mer sequences that are compared in the
sample and the reference sequence information are 9 to 20 nucleotides
adjacent to the occurrence of the anchor sequences. (See Appeal Br. 8.)
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that limitation does not make the collection and analysis other than abstract.”
SAP, 898 F.3d at 1168 (internal quotation marks omitted)).4
STEP 2B
Having concluded that Appellant’s claim 78 is directed to an abstract
idea under Step 2A of the Guidance, we turn to Step 2B of the Guidance.
Contrary to Appellant’s contention (Reply Br. 11), Step 2B requires that we
look to whether the claim “adds a specific limitation beyond the judicial
exception that [is] not ‘well-understood, routine, conventional’ in the field.”
Guidance 84 Fed. Reg. at 56 (emphasis added); MPEP § 2106.05(d); see
BSG Tech LLC v. BuySeasons, Inc., 899 F.3d 1281, 1290 (Fed. Cir. 2018)
(explaining that the Supreme Court in Alice “only assessed whether the

4 We agree with the Examiner that the claim also involves a naturally
occurring correlation, i.e., the characterization of an organism based solely
on the presence of sequence data that matches sequence data from a database
at a certain amount. The sequence information of the sample is a natural
phenomena and the relationship of that information to a phenotypic trait is
simply put a natural law. Nothing more than this observation is required by
the claims. In Mayo, the discovery underlying the claims was that when
blood levels were above a certain level harmful effects were more likely and
when they were below another level the drug’s beneficial effects were lost.
Mayo, 566 U.S. at 74–76. The claims provided that particular levels of
measured metabolite indicated a need to increase or decrease the amount of
drug subsequently administered to the subject. Id. at 75. However, the
claims did not require any actual action be taken based on the measured
level of metabolite. Id. at 75–76. Thus, the claims which required only the
observation of a natural law were deemed patent-ineligible. Similarly, here,
the claim requires only the observation of the natural law, and for this reason
too are properly deemed patent-ineligible.
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claim limitations other than the invention’s use of the ineligible concept to
which it was directed were well-understood, routine and conventional”).
“Even assuming [the claimed invention is novel], it does not avoid the
problem of abstractness.” Affinity Labs of Tex., LLC v. DIRECTV, LLC, 838
F.3d 1253, 1263 (Fed. Cir. 2016). That is because the inventive concept
must be significantly more than the abstract idea itself. Synopsys, Inc. v.
Mentor Graphics Corp., 839 F.3d 1138, 1151 (Fed. Cir. 2016) (“[A] claim
for a new abstract idea is still an abstract idea.”)
As discussed above, the additional elements recited in claim 78,
beyond the abstract idea to which it is directed, are the data-gathering step of
“receiving” nucleotide information from a sample as well as “trait-specific
reference sequence information comprising trait-specific nucleotide
sequences derived from thousands of microbial genomes” and the use of a
generic computer. Appellant’s Specification supports the Examiner’s
conclusion that these additional elements are well-understood, routine, and
conventional. (Final Action 6.) Appellant’s Specification indicates these
additional elements were well-understood, routine, and conventional
components because it describes them at a high level of generality and in a
manner that indicates that they are sufficiently well-known. In particular,
the Specification indicates employment of a generic processor in the system
(Spec. ¶ 84), the sequence information of the sample “may be in the form of
a sequence information file” (id. ¶¶ 88, 90), and the trait-specific sequence
information may be contained in a trait-specific database catalog in a
traditional reference database, such as GenBank (id. ¶ 100).
The recited computer, however, does not provide “significantly more”
than the abstract idea, because “the mere recitation of a generic computer
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cannot transform a patent-ineligible abstract idea into a patent-eligible
invention.” Alice, 573 U.S. at 223.
In light of the foregoing, we conclude that claim 78 is directed to no
more than judicial exceptions to Section 101 and does not recite the
“significantly more” requisite to transform the nature of the claim into a
patent-eligible application. We consequently affirm the Examiner’s
rejection upon this ground.
Claims 79–83 have not been argued separately and therefore fall with
claim 78. 37 C.F.R. § 41.37(c)(1)(iv).

DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
78–83 101 Eligibility 78–83

No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1). See 37 C.F.R.
§ 1.136(a)(1)(iv).

AFFIRMED