Ex Parte Homayouni et al

Patent Trial and Appeal Board

May 11, 2018

11215635 (P.T.A.B. May. 11, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
111215,635 08/30/2005
29973 7590 05/15/2018
CRGOLAW
ATTN: STEVEN M. GREENBERG, ESQ.
7900 Glades Road
SUITE 520
BOCA RATON, FL 33434
FIRST NAMED INVENTOR
Ramin Homayouni
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.
l 149-2U 4052
EXAMINER
LIN, JERRY
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
05/15/2018 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):
docketing@crgolaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte RAMIN HOMA YO UNI, MICHAEL WAITS EL BERRY,
KEVIN ERICH HEINRICH, and LAI WEI 1
Appeal2016-003142
Application 11/215,635
Technology Center 1600
Before ERIC B. GRIMES, FRANCISCO C. PRATS, and DAVID COTT A,
Administrative Patent Judges.
GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
and computer program product for determining gene relationships, which
have been rejected as being directed to patent-ineligible subject matter. We
have jurisdiction under 35 U.S.C. § 6(b ). We affirm.
STATEMENT OF THE CASE
The Specification states that "vector space modeling has been
explored for gene clustering using functional information in annotated
1 Appellants identify the Real Party in Interest as the University of
Tennessee Research Foundation. Appeal Br. 2.
Appeal 2016-003142
Application 11/215,635
indices or MEDLINE abstracts." Spec. i-f 9. "[A] variant of the vector space
model, referred to as 'Latent Semantic Indexing' (LSI), is shown to improve
information retrieval by a factor of thirty percent." Id. i-f 10. "[U]sing LSI,
relevant documents can be retrieved based on the degree of similarity in the
word usage patterns in the documents." Id.
The Specification discloses "automated methods for identifying gene
relationships based upon a modeling of textual information relating to gene
systems within gene documents." Id. i-f 2. "[G]ene documents can include a
collection of textual information obtained from public or private databases
such as full-text online journal articles, abstract citations in MEDLINE,
digital textbooks, and a variety of online gene centered indexes." Id. i-f 12.
"[T]he method, system and apparatus of the invention can utilize Latent
Semantic Indexing (LSI) to identify conceptually related genes based on the
textual information in the gene documents." Id.
Claims 1-8 and 13-20 are on appeal. Claim 1 is representative and
reads as follows:
1. A sementic gene organization method comprising:
producing in a text mining tool executing in memory by a
processor of a computer, gene documents for a plurality of
selected genes by compiling textual information included as
part of citations that cite to publications that have previously
been cross-referenced in a database for said selected genes;
processing by said processor in said memory said gene
documents according to a latent semantic indexing (LSI) model
to measure by said processor similarities between gene
documents based upon similar word usage patterns in the
textual information;
receiving in said computer a query vector of at least one
term; and,
2
Appeal 2016-003142
Application 11/215,635
parsing by said processor said gene documents to
produce a result set of semantically relevant gene relationships
responsive to receiving the query vector of at least one term.
DISCUSSION
The Examiner has rejected claims 1-8 and 13-20 under 35 U.S.C.
§ 101 on the basis that "[t]he claims are directed to the abstract idea of using
LSI to process gene documents." Final Action2 2. The Examiner finds that
"[t ]he additional elements or combination of elements in the claims other
than the abstract idea per se amount to no more than mere instructions to
implement the idea on a computer." Id. at 2-3. The Examiner concludes
that the "additional claim elements do not provide meaningful limitations to
transform the abstract idea into a patent eligible application of the abstract
idea." Id. at 3.
We agree with the Examiner that claim 1 is directed to a patent-
ineligible method. The Supreme Court has
set forth a framework for distinguishing patents that claim laws
of nature, natural phenomena, and abstract ideas from those that
claim patent-eligible applications of those concepts. First, we
determine whether the claims at issue are directed to one of
those patent-ineligible concepts. If so, we then ask, "[ w ]hat
else is there in the claims before us?" To answer that question,
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.
Alice Corp. Pty. Ltd. v. CLS Bank Int'!, 134 S. Ct. 2347, 2355 (2014)
(citations omitted).
2 Office Action mailed Feb. 26, 2015.
3
Appeal 2016-003142
Application 11/215,635
Here, claim 1 is directed to the abstract idea of applying Latent
Semantic Indexing (LSI) to published citations from existing databases to
identify related genes. So the next question is, what else is there in the
claims before us?
LSI has been in the prior art since at least 1989, when U.S. Patent
4,839,853 was issued. Spec. i-f 10. "The LSI model has been applied in
several different applications including essay grading and standardized
testing." Id. i-f 11. "LSI methods also have been applied to problems in the
biological and medical sciences." Id. "Recently it has been demonstrated
that LSI techniques can be used to visualize themes and relationships from
full-text articles in the scientific literature in order to understand the relations
among nominal fields of science." Id. A related method, vector space
modeling, "has been explored for gene clustering using functional
information in annotated indices or MEDLINE abstracts." Id. i-f 9.
In essence, the method of claim 1 amounts to no more than applying
the existing-routine and conventional-technique of LSI to a different kind
of data: "textual information included as part of citations that cite to
publications that have previously been cross-referenced in a database for ...
selected genes." Claim 1. "But merely selecting information, by content or
source, for collection, analysis, and display does nothing significant to
differentiate a process from ordinary mental processes, whose implicit
exclusion from § 101 undergirds the information-based category of abstract
ideas." Electric Power Group, LLC v. Alstom S.A., 830 F.3d 1350, 1355
(Fed. Cir. 2016). As in Electric Power Group, "[t]he claims in this case do
not even require a new source or type of information, or new techniques for
4
Appeal 2016-003142
Application 11/215,635
analyzing it." Id. "Merely requiring the selection and manipulation of
information ... by itself does not transform the otherwise-abstract processes
of information collection and analysis." Id.
We conclude that claim 1 is directed to the concept of applying LSI to
existing data regarding selected genes, and the steps recited in the claim
represent the routine and conventional steps of applying LSI to a specific
type of data. Therefore, the steps of the claimed method, even considered as
an ordered combination, do not transform the nature of the claim into a
patent-eligible application of the abstract idea to which claim 1 is directed.
See Alice Corp., 134 S. Ct. at 2355.
Appellants argue that the "invention presents the innovative concept
of semantic gene organization based upon the computerized identification of
conceptually related genes based upon computer parsed textual content of
gene documents." Appeal Br. 10. Appellants argue that i-fi-121-27 and
Figure 2 of the Specification show that
the innovative concept of Applicants' claims [is] achieved by
the complex interoperation of several computer processing
systems-a parser (element 210 of Figure 2 ), pre-process
(element 220 of Figure 2), a matrix generator (element 235 of
Figure 2), a document-to-document similarity processor
(element 265 of Figure 2) and a self-similarity matrix generator
(element 290 of Figure 2).
Id. at 13. Appellants conclude that, "[t]herefore, in contrast to the claims of
[Internet Patents Corp. v. Active Network, Inc., 790 F.3d 1343 (Fed. Cir.
2015)], because the innovative concept of Appellants' claims 1 through 20
are claimed and described as a whole to include how the innovative concept
is achieved, Appellants' claims 1 through 20 are statutory under the law."
Id.
5
Appeal 2016-003142
Application 11/215,635
This argument is not persuasive. The Internet Patents court noted that
[t]he two-step analytic protocol introduced in Mayo directs
attention to whether the claim contains an "inventive concept."
Determination of what is an inventive concept favors inquiries
analogous to those undertaken for determination of patentable
invention, for a known idea, or one that is routine and
conventional, is not inventive in patent terms.
Internet Patents, 790 F.3d at 1346.
The court held that "the character of the claimed invention is an
abstract idea: the idea of retaining information in the navigation of online
forms." Id. at 1348. The court noted that the specification of the patent
under consideration acknowledged that the Back and Forward navigation
functionalities recited in the claimed method were well-known and
conventional. Id. Similarly here, Appellants' Specification acknowledges
that the LSI model is known in the art and has previously been applied to
analyze a variety of data types, including visualizing relationships based on
articles in the scientific literature. Spec. i-fi-1 9-11.
The Internet Patents court noted that the patent's "claim 1 contains no
restriction on how the [desired] result is accomplished." 790 F.3d at 1348.
Similarly here, claim 1 contains no restriction on how the text of citations is
compiled in order to produce gene documents, or how those gene documents
are processed using LSI to measure similarities between them, or how a
query vector is generated, or how gene documents are parsed to produce a
result set of gene relationships.
Although Appellants point to the Specification's Figures 1 and 2,
those figures are merely "a block diagram of a semantic gene organization
system" and "a schematic illustration of a semantic gene organization tool,"
6
Appeal 2016-003142
Application 11/215,635
respectively. Spec. i-fi-f 17-18. They do not provide any description of how
the functions listed in the diagrams are carried out.
Appellants also point to the description of the disclosed method in the
Specification's i-fi-121-27, which provide algorithms for carrying out at least
some of the functions recited in Figure 2. However, none of the details
recited in i-fi-121-27 are included in claim 1, which therefore encompasses
any method of applying the LSI model to determine gene relationships based
on published information about genes in existing databases. In addition,
Appellants have not pointed to evidence that the Specification's description
of the disclosed method represents anything more than the routine and
conventional application of LSI to a particular type of information; in this
case, information in existing databases that relates to selected genes.
In summary, claim 1 is directed to an abstract idea and the additional
features of the claim do not transform the claimed method into a patent-
eligible application of the abstract idea. We therefore affirm the rejection of
claim 1 under 35 U.S.C. § 101. Claims 2-8 and 13-20 have not been argued
separately and therefore fall with claim 1. 37 C.F.R. § 41.37(c)(l)(iv).
SUMMARY
We affirm the rejection of claims 1-8 and 13-20 under 35 U.S.C.
§ 101.
7
Appeal 2016-003142
Application 11/215,635
TIME PERIOD FOR RESPONSE
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
8