Ex Parte Varpela et al

Board of Patent Appeals and Interferences

Sep 13, 2010

10883044 (B.P.A.I. Sep. 13, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte PERTTELI VARPELA and MEELIS KOLMER
____________

Appeal 2009-006156
Application 10/883,044
Technology Center 2100
____________

Before JOSEPH L. DIXON, JAY P. LUCAS, and STEPHEN C. SIU,
Administrative Patent Judges.

DIXON, Administrative Patent Judge.

DECISION ON APPEAL1

1 The two-month time period for filing an appeal or commencing a civil
action, as recited in 37 C.F.R. § 1.304, or for filing a request for rehearing,
as recited in 37 C.F.R. § 41.52, begins to run from the “MAIL DATE”
(paper delivery mode) or the “NOTIFICATION DATE” (electronic delivery
mode) shown on the PTOL-90A cover letter attached to this decision.

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The Appellants appeal under 35 U.S.C. § 134(a) from the Final
Rejection of claims 1-8. We have jurisdiction under 35 U.S.C. § 6(b).
We Affirm.

I. STATEMENT OF THE CASE
The Invention
The invention at issue on appeal relates to a method and an
Information Management System (IMS) for organizing and storing
biochemical information (Spec. 1).

The Illustrative Claim
Claim 1, an illustrative claim, reads as follows:
1. An information management system (IMS) comprising:

a server and a database, wherein:

the database is operable to store:

at least one of biomaterial information and pathway information;
and

location information that has a database relation to the at least
one of biomaterial information and pathway information;

wherein the location information comprises a multi-level
location hierarchy; and wherein the IMS comprises a user
interface which enables a user to view the location information
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as an information element distinct and independent from the
biomaterial information and/or pathway information.

The References
The Examiner relies on the following references as evidence:
Seilhamer US 6,023,659 Feb. 8, 2000
Tomomitsu US 6,944,513 B1 Sep. 13, 2005

Krishnamurthy et al. Pathway Database System: An integrated set of
tools for Biological Pathways SAC 2003, pp. 1-15 (hereafter
Krishnamurthy)

The Rejections
The following rejections are before us for review:
Claims 1-2, and 6-8 stand rejected under 35 U.S.C. § 103(a) as
being unpatentable over the combination of Seilhamer and
Krishnamurthy.
Claims 3-5 stand rejected under 35 U.S.C. § 103(a) as being
unpatentable over the combination of Seilhamer, Krishnamurthy, and
Tomomitsu.
Only those arguments actually made by the Appellants have been
considered in this decision. Arguments which the Appellants could have
made but chose not to make in the Briefs have not been considered and are
deemed to be waived. See 37 C.F.R. § 41.37 (c)(1)(vii) (2008).

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II. ISSUE
Has the Examiner erred in finding that the combination of Seilhamer
and Krishnamurthy teaches or fairly suggests “location information that has
a database relation to the at least one of biomaterial information and
pathway information” and “the location information comprises a multi-level
location hierarchy”, as recited in claim 1?

III. PRINCIPLES OF LAW
Scope of Claim
During prosecution before the USPTO, claims are to be given their
broadest reasonable interpretation, and the scope of a claim cannot be
narrowed by reading disclosed limitations into the claim. See In re Morris,
127 F.3d 1048, 1054 (Fed. Cir. 1997). The Office must apply the broadest
reasonable meaning to the claim language, taking into account any
definitions presented in the specification. In re Am. Acad. of Sci. Tech Ctr.,
367 F.3d 1359, 1364 (Fed. Cir. 2004) (citing In re Bass, 314 F.3d 575, 577
(Fed. Cir. 2002)).
“Giving claims their broadest reasonable construction ‘serves the
public interest by reducing the possibility that claims, finally allowed, will
be given broader scope than is justified.’” Id. (quoting In re Yamamoto, 740
F.2d 1569, 1571 (Fed. Cir. 1984)). “Construing claims broadly during
prosecution is not unfair to the applicant . . . because the applicant has the
opportunity to amend the claims to obtain more precise claim coverage.” Id.
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Obviousness
“Obviousness is a question of law based on underlying findings of
fact.” In re Kubin, 561 F.3d 1351, 1355 (Fed. Cir. 2009). The underlying
factual inquiries are: (1) the scope and content of the prior art, (2) the
differences between the prior art and the claims at issue, (3) the level of
ordinary skill in the pertinent art, and (4) secondary considerations of
nonobviousness. KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 406 (2007)
(citation omitted).

IV. FINDINGS OF FACT
The following findings of fact (FFs) are supported by a preponderance
of the evidence.
Seilhamer
1. Seilhamer discloses a location information organized based on a
“where” principle:
Preferably, the organizing principle of a hierarchy will be an
important aspect of gene function. For example, the biological
function hierarchy may be thought of as being organized on the
principle of "Why" a gene's function is important; and the
molecular hierarchy on the principle of for "What" a gene's
function is important. Other hierarchies might be organized on
a "Where" principle, such as a hierarchy based upon the
tissues, cells or subcellular locations in which proteins are
expressed, or a "When" principle, such as a hierarchy based
upon or temporal or developmental expression patterns.
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(col. 22, ll. 38-48, fig. 3) (Emphasis added).
2. Seilhamer further discloses utilizing a common end biological
function or pathway to categorize location hierarchy:
A biological function list preferably categorizes proteins by a
common end biological function or "pathway" such as
oncogenesis or apoptosis. The focus is more global than the
molecular function hierarchy. In a preferred embodiment, the
hierarchy includes a categories [sic] at multiple levels of focus
in biology. Examples of such levels include a cellular level, a
tissue level, and an organism level. An example of a cellular
level category is DNA repair, an example of a tissue level
category is apoptosis, and an example of an organism level
category is development.

(col. 22, l. 61-col. 23, l. 3) (Emphases added).

3. Selhamer also discloses a table 222 in the Fig. 3 (a preferred
embodiment of the present invention describes a physical data model for
gene expression relationship database) (col. 4, ll. 43-46) uniquely specifies
each protein function category “pathway” within the one or more hierarchies:
A table 220 denoted "FL_PFExternalHit" includes records which tie
external hits to specific protein function hierarchies. These hierarchies
and their applications will be described in more detail below. The
records in table 220 include the hit ID and hit type as described above,
and in addition a PF_ID (protein function identifier) which uniquely
specifies each category in the protein function hierarchies. Note that
the relation between table 218 and 220 is a one to many relationship.
This is because each unique hit from a public database (presented in
table 218) may fall under multiple categories within the protein
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function hierarchies allowed in table 220. The primary key of table
220 includes a combination of PF_ID, hit ID, and hit type.

A table 222 denoted “FL_ProteinFunction” uniquesly specifies each
protein function category within the one or more heierarchies
supported in this invention. The records of table 222 include a protein
function identifier (PF_ID) which uniquely identifies the categories of
the protein function hierarchies. This value may be displayed to users
viewing protein hierarchy information. In addition, the records of
table 222 include a protein function type (PF_Type) which uniquely
specifies which of the various hierarchies the particular category falls
under; an enzyme hierarchy, a molecular function hierarchy or a
biological function hierarchy, for example.

(Col. 18, ll. 35-59, fig. 3) (Emphases added).

V. ANALYSIS
The Appellants have the opportunity on appeal to the Board of Patent
Appeals and Interferences (BPAI) to demonstrate error in the Examiner’s
position. See In re Kahn, 441 F.3d 977, 985-86 (Fed. Cir. 2006) (citing In re
Rouffet, 149 F.3d 1350, 1355 (Fed. Cir. 1998)).
The Examiner sets forth a detailed explanation of a reasoned
conclusion of unpatentability in the Examiner’s Answer. Therefore, we look
to the Appellants’ Brief to show error in the proffered reasoned conclusion.
Id.
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Grouping of Claims

The Appellants have elected to argue claims 1-2 and 6-8 together as
a group (App. Br. 9). Therefore, we select independent claim 1 as the
representative claim for this group, and we will address the Appellants’
arguments with respect thereto. 37 C.F.R. § 41.37 (c)(1)(vii). See In re
Nielson, 816 F.2d 1567, 1572 (Fed. Cir. 1987).

35 U.S.C. § 103(a) rejections

With respect to claim 1, the Appellants contend that Seilhamer fails to
teach location information comprising a multi-level location hierarchy
because “Seilhamer fails to teach a combination of multiple principles, such
as specifying ‘what’ and ‘where’.” (App. Br. 8). The Appellants further
contend “Seilhamer’s teaching of a ‘hierarchy organized on a where
principle’. . . must be interpreted a biomaterial hierarchy not a location
hierarchy” because “prior art techniques for managing biological
information are based on the assumption that biomaterial and location are
interchangeable: one necessarily determines the other. However,
Appellants’ invention is partially based on the discovery that this simplistic
assumption is not always applicable. . . SBML (like Seilhamer) fails to
provide for creation of ‘location information’ as an information element
distinct and independent from the ‘biomaterial information and/or pathway
information.’” (Id. 8-9).
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We disagree with the Appellants’ contentions. We start our analysis
with claim construction. We, in light of the Specification, broadly yet
reasonably construe the claim limitation “location information comprises a
multi-level location hierarchy” as any location information of biomaterial
that comprises more than one level hierarchy because there is no limitation
in the claim language to prevent us from reading the language broadly.
Claim 1 recites “location information comprises a multi-level location
hierarchy” or an “interface which enables a user to view the location
information as an information element distinct and independent from the
biomaterial information and/or pathway information.” (Emphases added).
The claim language of claim 1 does not require a combination of multiple
principles, nor require the creation of location information as an
information element distinct and independent from the biomaterial
information and/or pathway information (only require an interface allows a
user to view the location information distinctly and independently from the
biomaterial information and/or pathway information). Thus, the contentions
of Appellants are not commensurate to the scope of claim 1. Nevertheless,
we find Seilhamer teaches that the location information organized based on
“where” principle has multi-level hierarchy based on the tissues, cells, and
subcellular locations (FF 1), which clearly reads on “location information
comprises multi-level location hierarchy”, as recited in claim 1, under our
claim construction.
The Appellants further contend that Seilhamer fails to teach or suggest
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that claimed location information has a database relation to at least one of
biomaterial and pathway information (App. Br. 10). According to the
Appellants, the Fig. 3 of Seilhamer “relates to organizing sequence
information imported from external sources.” (Id.), and the use of terms
“location” and “relation” “are in completely disconnected passages of
Seilhamer and do not pertain to each other at all.” (Id. 11).
We disagree with the Appellants’ contentions. We find that Fig. 3 is a
physical data model of biomaterial (gene sequence) of the present invention,
which is not information from external sources (FF 3). We also find that
Seilhamer teaches utilizing pathway information to categorize the multi-
level hierarchy location information (FF 2). As a protein function identifier
identifies or uniquely specifies the categories within hierarchies of the
location information in the table 222, a database relation is established
between the multi-level hierarchy of the location information and pathway
information (FF 3), which also reads on claim 1. We, thus, find the
Appellants’ arguments are not persuasive.
Therefore, we conclude that the combination of Seilhamer and
Krishnamurthy teaches or fairly suggests the argued limitations of the claim
1.
Accordingly, we sustain the Examiner’s obviousness rejection of
claim 1. Independent claim 8 contains similar limitations, and the
Appellants present similar arguments thereto. We also sustain the
Examiner’s obviousness rejection of dependent claims 2-7, which have not
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been separately argued, and fall with their base claims. 37 C.F.R. § 41.37
(c)(1)(vii). See In re Nielson, 816 F.2d 1567, 1572 (Fed. Cir. 1987).
VII. CONCLUSION
Accordingly, based on our consideration of the totality of the record
before us, we have weighed the evidence of obviousness found in the
combined teachings of the applied references, with Appellants’
countervailing evidence and arguments for nonobviousness and conclude
that the claimed invention encompassed by appealed claims 1-8 would have
been obvious as a matter of law under 35 U.S.C. § 103(a).

VII. ORDER
We affirm the obviousness rejections of claim 1-8 under 35 U.S.C.
§ 103(a).
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136 (a). See 37 C.F.R.
§ 1.136(a)(1)(iv).
AFFIRMED

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