Ex Parte Homayouni et al

Patent Trial and Appeal Board

Oct 16, 2012

11215635 (P.T.A.B. Oct. 16, 2012)

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.
11/215,635 08/30/2005 Ramin Homayouni 1149-2U 4052
29973 7590 10/17/2012
CAREY, RODRIGUEZ, GREENBERG & O''KEEFE LLP
ATTN: STEVEN M. GREENBERG, ESQ.
950 PENINSULA CORPORATE CIRCLE
SUITE 2022
BOCA RATON, FL 33487
EXAMINER
LIN, JERRY
ART UNIT PAPER NUMBER
1631
MAIL DATE DELIVERY MODE
10/17/2012 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 RAMIN HOMAYOUNI, MICHAEL WAITSEL BERRY,
KEVIN ERICH HEINRICH, and LAI WEI
__________

Appeal 2011-011269
Application 11/215,635
Technology Center 1600
__________

Before LORA. M. GREEN, MELANIE L. McCOLLUM, and STEPHEN
WALSH, Administrative Patent Judges.

McCOLLUM, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a
sementic gene organization method and computer program product. The
Examiner has rejected the claims as obvious. We have jurisdiction under
35 U.S.C. § 6(b). We affirm.
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STATEMENT OF THE CASE
Claims 1-8 and 13-20 are on appeal (App. Br. 2 & 4).
1
The claims
subject to each rejection have not been argued separately and therefore stand
or fall together. 37 C.F.R. § 41.37(c)(1)(vii). Claims 1 and 8 are
representative and read as follows:
1. A sementic gene organization method comprising:
producing in a text mining tool executing in a computer, gene
documents for a plurality of selected genes by compiling textual information
for citations which are cross-referenced in a database for said selected genes;
processing said gene documents according to a latent semantic
indexing (LSI) model to measure similarities between gene documents based
upon similar word usage patterns; and,
parsing said gene documents to produce a result set of semantically
relevant gene relationships responsive to receiving a query vector of at least
one term.
8. The method of claim 1, further comprising producing said query
vector according to one of a keyword query and a gene document query.
Claims 1-6 and 13-18 stand rejected under 35 U.S.C. § 103(a) as
obvious over Stuart
2
in view of Glenisson
3
(Ans. 5-6).
Claims 7, 8, 19, and 20 stand rejected under 35 U.S.C. § 103(a) as
obvious over Stuart in view of Glenisson and Deerwester
4
(Ans. 7).

1
Claims 9-12 are also pending but have been withdrawn from consideration
(App. Br. 2).
2
Gary W. Stuart et al., Integrated gene and species phylogenies from
unaligned whole genome protein sequences, 18 BIOINFORMATICS 100-108
(2002).
3
Patrick Glenisson et al., Meta-Clustering of Gene Expression Data and
Literature-based Information, 5 SIGKDD EXPLORATIONS 101-112 (2003).
4
Scott Deerwester et al., Indexing by Latent Semantic Analysis, 41 J. AM.
SOC’Y INFO. SCI. 391-407 (1990).
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The Examiner relies on Stuart for teaching “a computer method of
determining gene relationships where genomes are processed according to a
latent semantic indexing model using a text mining tool . . . ; producing a
result set of semantically relevant gene relationships” (id. at 6). However,
the Examiner finds that Stuart “does not teach using a gene document” (id.).
The Examiner relies on Glenisson for teaching:
creating a computer gene document . . . ; where the textual
information for citations are [compiled] from various adopted
information sources . . . ; where the adopted information
sources contain cross references for the selected genes in a
database . . . ; and parsing the documents to produce a result set
of semantically relevant gene relationships responsive to a
query vector.
(Id.)
The Examiner concludes:
It would have been obvious for one of ordinary skill in the art at
the time of the invention to use the gene document of Glenisson
et al. with the method of Stuart et al. to gain the benefit of an
integrated analysis of expression data with literature extracted
information. Glenisson et al. teach that expression data with
literature extracted information shows biologically meaningful
gene clusters that would otherwise not be revealed. Thus, one
of ordinary skill in the art would have been motivated to use the
gene documents of Glenisson et al. with the method of Stuart et
al. to find new biologically meaningful gene clusters.
(Id. at 7.)
In rejecting claims 7, 8, 19, and 20, the Examiner additionally relies
on Deerwester for teaching “using a keyword query and a document query”
(id. at 7-8).
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ISSUE
With regard to both grounds of rejection, the issue raised by
Appellants is: Does the evidence support the Examiner’s conclusion that it
would have been obvious to produce gene documents for a plurality of
selected genes by compiling textual information for citations which are
cross-referenced in a database for the selected genes?
FINDINGS OF FACT
1. The Specification states that “gene 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 such as
LocusLink (Gene) and OMIM databases” (Spec. ¶ [0012] (emphasis
added)).
2. The Specification also states that “one or more gene documents
110 can be produced for selected genes by compiling textual information,
for example titles and abstracts, for citations which are cross-referenced in
any public or private database for the selected genes” (id. at ¶ [0020]).
3. In addition, the Specification states:
Figure 3 is a flow chart illustrating a process for identifying
conceptually related genes based upon the textual content of
gene documents in the semantic gene organization system of
Figure 1. Beginning first in block 310, citations can be located
which are cross-referenced in biotechnical databases such as
LocusLink. For example, the cross-references can include each
of human, mouse and rat entries for a specific gene. In
block 320 the titles and abstracts for the located citations can be
compiled into corresponding gene documents.
(Id. at ¶ [0028].)
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4. The Examiner relies on Glenisson, specifically at page 102, for
teaching the production of gene documents (Ans. 6 & 9).
5. Glenisson teaches:
In Figure 1 we give an overview of our approach: starting from
a literature repository we compute a document index based on
the vector space model which results in a document-term
matrix. For each gene we summarize all documents that are
linked to it (e.g., as query results from PUBMED or as entries
in a curated gene-literature repository) by merging the
associated information.
(Glenisson 102.)
6. Glenisson also teaches: “Our text-based information source
consists of a literature index for yeast genes constructed from a corpus of
24,909 yeast-related MEDLINE abstracts. These abstracts and their gene
associations were extracted from the curated literature references available
in the Saccharomyces Genome Database as of 11 Jan 2003.” (Id. (footnote
removed).)
ANALYSIS
Appellants generally argue that the Examiner has “failed to meet the
express requirements of 37 C.F.R. § 1.104(c),” which states: “When a
reference is complex or shows or describes inventions other than that
claimed by the applicant, the particular part relied on must be designated as
nearly as practicable. The pertinence of each reference, if not apparent, must
be clearly explained and each rejected claim specified.” (App. Br. 6.)
Specifically, Appellants argue that the “Examiner has made no attempt at
locating the following” claim feature: compiling textual information for
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citations which are cross-referenced in a database for selected genes (id. at
8-9). We are not persuaded.
The Examiner relies on Glenisson, specifically at page 102, for
teaching the production of gene documents (Finding of Fact (FF) 4). We
have reviewed Glenisson page 102 (see, in particular, FF 5-6). We have also
reviewed the description of gene documents in Appellants’ Specification
(see, in particular, FF 1-3). We conclude that the evidence supports the
Examiner’s position that Glenisson teaches producing gene documents, that
is, “a collection of textual information obtained from public or private
databases” (FF 1), for a plurality of selected genes (i.e., yeast genes (FF 6)),
by compiling textual information for citations, that is, the MEDLINE
abstracts (FF 6), which are cross-referenced in a database for the selected
genes (FF 1).
CONCLUSION
The evidence supports the Examiner’s conclusion that it would have
been obvious to produce gene documents for a plurality of selected genes by
compiling textual information for citations which are cross-referenced in a
database for the selected genes. We therefore affirm the obviousness
rejections.
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
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