Ex Parte Sweeney

Patent Trials and Appeals Board

Jun 24, 2019

12800993 - (D) (P.T.A.B. Jun. 24, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/800,993 05/27/2010
7590 06/25/2019
Daniel Leo Sweeney
1314 N. Highland Avenue
Arlington Heights, IL 60004
FIRST NAMED INVENTOR
Daniel Leo Sweeney
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.
4304
EXAMINER
KOSACK, JOSEPH R
ART UNIT PAPER NUMBER
1626
MAIL DATE DELIVERY MODE
06/25/2019 PAPER
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.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte DANIEL LEO SWEENEY
Appeal2017-011142
Application 12/800,993
Technology Center 1600
Before JEFFREY N. FREDMAN, RICHARD J. SMITH, and
RYAN H. FLAX, Administrative Patent Judges.
FREDMAN, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal 1,2 under 35 U.S.C. § 134 involving claims to a data
structure of molecules composed of a set of partitions of subgroups of exact
mass. The Examiner rejected the claims as anticipated, as obvious, and as
directed to patent-ineligible subject matter. We have jurisdiction under 35
U.S.C. § 6(b). We reverse the anticipation and obviousness rejections, but
affirm patent eligibility rejection.
1 Appellant is pro se and identifies the real party in interest as Daniel Leo
Sweeney (see App. Br. 1, 13).
2 We have considered and refer to the Specification of May 27, 2010
("Spec."); Final Office Action of Jan. 27, 2016 ("Final Act."); Appeal Brief
of June 22, 2016 ("App. Br."); and Examiner's Answer of Sept. 15, 2016
("Ans."). An oral hearing was held on May 23, 2019.
Appeal2017-011142
Application 12/800,993
Statement of the Case
Background
"When used to identify an unknown organic compound, a mass
spectrometer is basically an instrument that physically breaks up the
unknown organic compound into connected groups of atoms called
fragments, and then 'weighs' the fragments that are produced" (Spec. 1 ).
"The classical approach for identifying known compounds from their mass
spectral data is library matching. A mass spectral library is a computer file
containing a summary of the fragment masses and intensities of a large
number of compounds that have been previously analyzed by mass
spectrometry" (Spec. 2).
"Systematic bond-disconnection had been used to assign accurate-
mass fragments to known compounds .... Breakable bonds in a molecule
are assigned a penalty score based on the likelihood that the bond will
break" (Spec. 4). "The bonds are then systematically broken ... and the
masses and elemental compositions of the resulting pieces were found"
(Spec. 4).
The masses of the fragment ions, obtained from the mass
spectral data, are then compared to the calculated masses taking
into account that the mass may differ by the number of
hydrogens lost or gained in forming the fragment ion. If
multiple pieces had the same mass and formula, the
corresponding partial structures would be displayed.
(Spec. 4). "Partitioning and systematic bond disconnection, required for
searching this way, are both very CPU intensive, especially for larger
molecules with more bonds and more partitions" (Spec. 5).
The Specification explains that the inventive method has advantages
of speed and simplicity over the prior art (see Spec. 50).
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Application 12/800,993
The Claims
Claims 1-12 are on appeal. Independent claim 1 is representative and
reads as follows:
1. A computer readable non-transitory medium encoded
with representations of molecules as:
a set of partitions of subgroups of exact mass which
comprise said molecules.
The Re} ections
A. The Examiner rejected claims 1-12 under 35 U.S.C. § 102(b) as
anticipated by Colby3 (Ans. 4--5).
B. The Examiner rejected claims 1-12 under 35 U.S.C. § 103(a) as
obvious over Colby (Ans. 5-6).
C. The Examiner rejected claims 1-12 under 35 U.S.C. § 101 as directed
to patent ineligible subject matter (Ans. 2--4).
Claim Interpretation
We begin with claim interpretation, because before a claim is properly
interpreted, its scope cannot be compared to the prior art or analyzed for
patent eligibility.
"whereby clause"
The ambiguity at issue here is the presence of a clause after the final
period of final claim 12. The clause reads "whereby, an unknown
compound can be rapidly identified or characterized by comparing the
masses of its fragment ions, measured on a mass spectrometer, to said
3 Colby College Chemistry, http://www.colby.edu/chemistry/PChem/
Fragment.html (1997) ("Colby").
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Application 12/800,993
representations." The issue before us is whether this clause is part of one or
more of the claims or is not part of any of the claims.
The Manual of Patent Examining Procedure (MPEP) § 608.0l(m)
states: "Each claim begins with a capital letter and ends with a period.
Periods may not be used elsewhere in the claims except for abbreviations."4
Thus, consistent with the MPEP, claims end with a period. Therefore, any
text after a period, such as the "whereby" clause discussed above, is not
reasonably part of any of the claims. We therefore interpret the claims as
not including the "whereby" recitation.
"set of partitions of subgroups of exact mass"
The Specification consistently uses the term "set" in the common
usage as a collection of distinct objects, here subgroups. Claim 1 uses the
plural form of "subgroups," not the singular form "subgroup." Therefore,
claim 1 is reasonably interpreted as requiring the "set of partitions" to
include at least two "subgroups." See Dayco Products, Inc. v. Total
Containment, Inc., 258 F.3d 1317, 1327-28 (Fed. Cir. 2001) ("In accordance
with standard dictionary definitions, we have held that 'plurality,' when used
in a claim, refers to two or more items, absent some indication to the
contrary.")
Rejections A. and B. 35 U.S.C. § 102(b)/103(a) over Colby
The Examiner finds
Colby College Chemistry teach a computer readable non-
transitory medium encoded with representations of molecules
as a set of partitions with the exact masses, and include the
exact mass of a hydrogen atom for a broken single bond or two
4 An online MPEP is at https://mpep.uspto.gov/RDMS/MPEP/current.
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Application 12/800,993
hydrogen atoms for a broken double bond by virtue of the M +
1 and M + 2 readings.
(Final Act. 7). The Examiner relies upon the same reasoning in the
obviousness analysis (see Final Act. 8).
Appellant responds that in Colby, the Examiner redefines the M+ 1
and M+2 as "exact mass of a hydrogen atom and partitions" and in the
Examiner's rejection "the M+ 1 and M+2 terms are never used for what they
truly are - the relative abundances of the first two isotopes" (Ans. 10).
We agree with Appellant. As noted in our claim interpretation above,
the prior art must show at least two "subgroups of exact mass" to satisfy the
limitation of claim 1. In Colby, the only measurement of mass is shown in
the MM column, where, for example, the molecular mass of HN20 is shown
as 45.0089. The M+ 1 and M+2 columns are not molecular masses as the
values are too low, and Appellant's unrebutted statement that these refer to
isotopes, not mass, is persuasive. Therefore, the Colby reference neither
anticipates nor renders obvious the current claims because while Colby has
one column with one subgroup of exact mass, Colby does not teach at least
two subgroups of exact mass as required by claim 1. We therefore reverse
the anticipation rejection.
As to obviousness, the Examiner provides no persuasive reasoning
that explains why multiple columns of molecular mass would be included in
the Colby data. The Examiner has the initial burden of establishing a prima
facie case obviousness under 35 U.S.C. § 103. In re Oetiker, 977 F.2d 1443,
1445 (Fed. Cir. 1992). We therefore reverse the obviousness rejection.
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Application 12/800,993
C. 35U.S.C.§101
The Examiner finds "the claims are drawn to the abstract idea of a
table of masses of fragments of a compound" (Ans. 3). The Examiner
further finds the "fragments are caused via a natural phenomenon, namely
ionization of a particular compound" (id. at 9). The Examiner concludes
that "identification of a compound based on its natural fragmentation pattern
is not significantly more than the judicial exceptions against the patenting of
abstract ideas and laws of nature" (id. at 10).
Appellant responds that the
invention and claim( s) are for a data structure - not a
compilation of fragment masses into a fragmentation table. The
data structure is physically present on a non-transitory medium.
There are also logical relationships between the masses in each
partition and between those masses and the structure of the
chemical substance which those masses represent.
(App. Br. 6). Appellant asserts that "[f]unctional data structures have been
ruled patentable subject matter" (id.; citing In re Lowry, 33 F.3d 1579 (Fed.
Cir. 1994). Appellant cites Judge Mayer's concurrence in Ultramercial for
the proposition that the "Court would hold that abstractions that are
representations of chemical substances would meet the test of patentability"
(id. at 7, citing Ultramercial, Inc. v. HULU, LLC, 772 F.3d 709 (Fed. Cir.
2014)). Appellant also points to the "whereby" clause and contends that the
"claims are thus limited to a specific practical application of an idea" (id. at
8).
The Alice Test
As stated by the Supreme Court in Alice:
Section 101 of the Patent Act defines the subject matter
eligible for patent protection. It provides:
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"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.
"We have long held that this provision contains an important
implicit exception: Laws of nature, natural phenomena, and
abstract ideas are not patentable." Association for Molecular
Pathology v. Myriad Genetics, Inc., 569 U.S. [576], [589], 133
S.Ct. 2107, 2116, 186 L.Ed.2d 124 (2013).
Alice Corp. Pty. v. CLS Bankint'l, 573 U.S. 208,216 (2014). The
significance of these exceptions to patent-eligibility is to cast some shade on
the "anything under the sun" concept of what can be patented and to
foreclose patent applicants from obtaining patents covering the building
blocks of human ingenuity without integrated them into something more
( e.g., some practical implementation, such as using math to better
manufacture rubber). 5
5 We direct Appellant's attention to another Supreme Court decision in
Diamond v. Diehr, 450 U.S. 175 (1981). In Diehr, a similar dispute was at
issue over claims that recited a mathematical equation, the Arrhenius
equation, as used in a method of operating a rubber-molding press with the
aid of a computer. Id. at n.5. The Diehr Court is clear that reciting a
mathematical equation is reciting an abstract idea and pure math ( or
algorithm) is not patent eligible. Id. at 186 ( citing Gottschalk v. Benson, 409
U.S. 63 (1972) ). Reciting the performing of a mathematical calculation to
obtain mere data, e.g., an alarm limit, is also seen as claiming no more than
the abstract idea. Id. at 186--87 (citing Parker v. Flook, 437 U.S. 584
(1978)). However, even though the patent in Diehr expressly recited a
mathematical equation, it integrated it into a process for actually molding
rubber so that the math allowed the press to be opened at just the right time.
This was the use of an abstract idea integrated into a practical application
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To determine whether a claim is invalid under § 101, we employ the
two-step Alice framework. In Alice step one, we ask whether the claims are
directed to a patent ineligible concept. Id. at 218. Claims that are directed
only to abstract ideas, mathematical concepts and/or natural phenomena are
directed to patent ineligible concepts. Ariosa Diagnostics, Inc. v. Sequenom,
Inc., 788 F.3d 1371, 1376 (Fed. Cir. 2015). In Alice step two, we examine
the elements of the claims to determine whether they contain an inventive
concept sufficient to transform the claimed judicial exception into a patent-
eligible application. Mayo Collaborative Services v. Prometheus
Laboratories, Inc., 566 U.S. 66, 71-72 (2012) (quoting Alice, 573 U.S. at
218).
2019 Guidance
The PTO recently published revised guidance on the application of
§ 101. USPTO's January 7, 2019 Memorandum, 2019 Revised Patent
Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (2019) ("2019
Guidelines"). Under that guidance, we first look to whether the claim
recites:
( 1) any judicial exceptions, including certain groupings of abstract
ideas (i.e., mathematical concepts, certain methods of organizing
human activity such as a fundamental economic practice, or mental
processes); and
(2) additional elements that integrate the judicial exception into a
practical application (see MPEP § 2106.05(a}-(c), (e}-(h)).
and, so, the claim was not directed to the abstract idea and was patent-
eligible. Id. at 187.
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See 84 Fed. Reg. 54--55. Only if a claim (1) recites a judicial exception and
(2) does not integrate that exception into a practical application, do we then
look to whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not
"well-understood, routine, conventional" in the field (see MPEP
§ 2106.05(d)); or
( 4) simply appends well-understood, routine, conventional activities
previously known to the industry, specified at a high level of
generality, to the judicial exception.
See 84 Fed. Reg. 51.
Analysis
Applying Alice step one, we look to see if the claim recites any
judicial exceptions. Because, as discussed in our claim construction above,
the "whereby" clause, which discusses measuring using a mass
spectrometer, is not part of the claim, claim 1 is drawn to organized
molecular mass data on a computer readable medium. As the Specification
explains, a "computerized representation of a molecule is a file format for
holding information about a molecule in such a way that a data processing
means can manipulate the information in the file" (Spec. 3). The
Specification describes that:
In the preferred embodiment, a molecule is represented by a set
of partitions of subgroups of exact mass which comprise the
molecule, where said exact masses of subgroups include the
exact mass of a hydrogen atom in place of a broken single bond
or the mass of two hydrogen atoms in place of a broken double
bond.
(Spec. 6). That is, the described preferred and claimed embodiment
represents columns of data representing natural fragments of a starting
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molecule that, when added up in a single row, total the mass of the original
starting molecule ( adjusted for hydrogen atoms added by the bond breaking).
Thus, the claim is to a set of data.
While the intended use of the data represents pieces that are added
together to obtain masses that are then compared to unknown masses
detected in a mass spectrometry device, the data itself represents fragments
that naturally result when the mass spectrometer "physically breaks up the
unknown organic compound into connected groups of atoms called
fragments" (Spec. 1 ).
As explained by our reviewing court, "analyzing information ... by
mathematical algorithms, without more, [ are treated] as essentially mental
processes within the abstract-idea category." Elec. Power Grp., LLC v.
Alstom S.A., 830 F.3d 1350, 1354 (Fed. Cir. 2016). Because claim 1 recites
data subject to use in a mathematical algorithm, we find claim 1 recites a
mental process in the abstract idea category of judicial exceptions. In
addition, the data in claim 1 represents a natural result of bond breaking and
is therefore a "natural phenomena" because the "claim is concerned
primarily with the information contained ... not with the specific chemical
composition of a particular molecule." Myriad, 569 U.S. at 593.
A claim that recites a judicial exception requires further analysis to
determine if any additional elements integrate the judicial exception into a
practical application. See 84 Fed. Reg. 54. The 2019 Guidelines explain
that additional elements that integrate the judicial exception into a practical
application include applying the judicial exception in some meaningful way
beyond generally linking the use of the judicial exception to a particular
technological environment. (See 84 Fed. Reg. 55, citing Diehr, 450 U.S.
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175). For example, the claims in Diehr recited a method for operating a
rubber-molding press including the step of "opening the press automatically
when said comparison [ of calculated cure time vs. elapsed time] indicates
equivalence." See Diehr, 450 U.S. 179 n.5.
In this case, based on our interpretation of claim 1 as not including the
"whereby" clause, we find that claim 1 does not recite a practical application
of the data structure. There is no step in claim 1 that is analogous to the
Diehr step of opening the press because claim 1 lacks any specific, practical
physical act in a particular technological environment. At best, claim 1
represents naturally occurring data that might be used in a mathematical
analysis, but claim 1 does not require such a use. Because we conclude that
the judicial exceptions recited in claim 1 are not integrated into the practical
application of analyte detection systems, we conclude that claim 1 is not
directed to patent-eligible subject matter.
Our position is consistent with other recent Federal Circuit cases such
as In re TL! Commc'ns LLC Patent Litig., 823 F.3d 607, 610 (Fed. Cir.
2016). In TL!, the claimed method was drawn to "the concept of classifying
an image and storing the image based on its classification." Id. at 611. The
method created an "environment in which to carry out the abstract idea of
classifying and storing digital images in an organized manner." Id. at 611.
TL! found that "attaching classification data, such as dates and times, to
images for the purpose of storing those images in an organized manner is a
well-established 'basic concept' sufficient to fall under Alice step 1." Id. at
613.
The current claims lack the method steps recited in TL! and are
limited to something roughly analogous to the TL! classification of data
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itself. Just as the "classification data" in TL! is used to improve the speed of
classifying digital images, the data structure of claim 1 is intended ( though
not required by any specific claim language) to be used with and to improve
mass spectrometry analysis because "searching is very fast and the
representations are relatively small files" (Spec. 25). However, the
Specification acknowledges that fragment mass data was already known,
teaching the "classical approach for identifying known compounds from
their mass spectral data is library matching. A mass spectral library is a
computer file containing a summary of the fragment masses" (Spec. 3). We
recognize that claim 1 is intended to differ from these prior computer files in
the particular way the data is structured. However, the breadth of claim 1 as
encompassing any set of partitions of subgroups of exact mass does not
clearly distinguish the claimed data structure from the basic concept of
fragment files in the prior "summary of the fragment masses" (Spec. 3).
We also find these facts similar to those in Interval Licensing LLC v.
AOL, Inc., 896 F.3d 1335 (Fed. Cir. 2018). In Interval, the court found that
"acquiring and organizing information, as broadly recited by some of the
instructions limitations, is an abstract idea, not an improvement in how
computers and networks carry out their basic functions." Interval, 896 F.3d
at 1345. This reasoning applies to Appellant's claim 1, because claim 1 is
drawn to information itself that is organized in a particular format. 6 As in
Interval, instant claim 1 does "not convert, the abstract idea [ of organizing
6 We do not address the question of whether a claim written to use this
information in an improved mass spectrometry method, particularly a
method claim, would overcome the abstract idea concerns by integrating
those ideas into a practical improvement in the device itself because
currently none of the claims include such limitations.
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molecular data into subgroups] ... into a particular conception of how to
carry out that concept." Id. at 1346.
Alice Step Two
Because we determine that claims 1-12 are directed to judicial
exceptions, we apply Alice step two to evaluate whether the claim provides
an inventive concept, i.e., whether additional claim elements amount to
significantly more than the patent-ineligible exception itself. (See 2019
Guidelines, 84 Fed. Reg. at 56.) The Examiner finds
the additional elements present in the claims do not amount to
significantly more than the judicial exception. The additional
elements are either drawn to compound identifiers, adding
hydrogen atoms in order to identify particular fragments,
adding masses together, replacing non-contiguous subgroups
with the number zero, and replacing the sum of masses with the
exact mass of the molecule. The additional elements are
present in the abstract idea of mass spectrum analysis where
peaks are identified by mass number, and added together in
order to yield the identification of the compound analyzed.
(Ans. 3--4).
Appellant contends that the "fragmentation data referred to in this
patent application refers to mass spectral data obtained on a mass
spectrometer"; that "patent application briefly described and included two C
programs complete with source code that demonstrated how the invention
could be used to rapidly identify a molecule"; and that based on the
"whereby" clause "claims are thus limited to a specific practical application
of an idea, and the scope of the Applicant's claims is commensurate with the
invention's practical, real-world contribution" (App. Br. 6, 8)
We are not persuaded by Appellant's arguments because these argued
limitations are not part of the claims. As already discussed, the "whereby"
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clause was not incorporated into any claims and therefore is not part of, and
does not limit, any of the claims. In addition, claim 1 lacks any recitation to
a mass spectrometer or to any code that would be used to rapidly identify a
molecule. See In re Self, 671 F.2d 1344, 1348 (CCPA 1982) ("[A]ppellant's
arguments fail from the outset because ... they are not based on limitations
appearing in the claims.")
As to Appellant's general argument, the Specification states that a
"classical approach for identifying known compounds from their mass
spectral data is library matching. A mass spectral library is a computer file
containing a summary of the fragment masses and intensities of a large
number of compounds that have been previously analyzed by mass
spectrometry" (Spec. 2). Thus, the Specification acknowledges that using
computer files with fragment mass data is conventional. See Berkheimer v.
HP, Inc., 881 F.3d 1360, 1368 (Fed. Cir. 2018). There is no dispute that
computers, databases, and mass spectrometry devices were well known in
the prior art. Therefore, even if the abstract idea recited in claim 1 is novel,
"[a]ppending rote conventional activity in this way to an abstract idea does
not amount to an inventive concept." Interval, 896 F.3d at 1348.
Conclusion of Law
We conclude that claims 1-12 are directed to patent-ineligible subject
matter.
SUMMARY
We reverse the rejection of claims 1-12 under 35 U.S.C. § 102(b) as
anticipated by Colby.
We reverse the rejection of claims 1-12 under 35 U.S.C. § 103(a) as
obvious over Colby.
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We affirm the rejection of claims 1-12 under 35 U.S.C. § 101 as
directed to patent ineligible subject matter.
AFFIRMED
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