Acceptance, Processing, Use and Dissemination of Chemical and Three-Dimensional Biological Structural Data in Electronic Format, 35573-35577 [05-12199]
Download as PDF
<![CDATA[
Federal Register / Vol. 70, No. 118 / Tuesday, June 21, 2005 / Proposed Rules
Estimated Time Per Response: 22
minutes to 10 hours and 45 minutes.
Estimated Total Annual Burden
Hours: 4,171,568 hours.
Needs and Uses: The purpose of this
information collection is to permit the
Office to determine whether an
application meets the criteria set forth
in the patent statute and regulations.
The standard Fee Transmittal form, New
Utility Patent Application Transmittal
form, New Design Patent Application
Transmittal form, New Plant Patent
Application Transmittal form,
Declaration, Provisional Application
Cover Sheet, and Plant Patent
Application Declaration will assist
applicants in complying with the
requirements of the patent statute and
regulations, and will further assist the
Office in processing and examination of
the application.
Interested persons are requested to
send comments regarding these
information collections, including
suggestions for reducing this burden, to
Robert J. Spar, Director, Office of Patent
Legal Administration, Commissioner for
Patents, P.O. Box 1450, Alexandria, VA
22313–1450, or to the Office of
Information and Regulatory Affairs,
Office of Management and Budget, New
Executive Office Building, Room 10235,
725 17th Street, NW., Washington, DC
20503, Attention: Desk Officer for the
Patent and Trademark Office.
Notwithstanding any other provision
of law, no person is required to respond
to nor shall a person be subject to a
penalty for failure to comply with a
collection of information subject to the
requirements of the Paperwork
Reduction Act unless that collection of
information displays a currently valid
OMB control number.
List of Subjects in 37 CFR Part 1
Administrative practice and
procedure, Courts, Freedom of
Information, Inventions and patents,
Reporting and record keeping
requirements, Small Businesses.
For the reasons set forth in the
preamble, 37 CFR Part 1 is proposed to
be amended as follows:
(c) An applicant seeking to abandon
an application to avoid publication of
the application (see § 1.211(a)(1)) must
submit a declaration of express
abandonment by way of a petition under
this paragraph including the fee set
forth in § 1.17(h) in sufficient time to
permit the appropriate officials to
recognize the abandonment and remove
the application from the publication
process. Applicants should expect that
the petition will not be granted and the
application will be published in regular
course unless such declaration of
express abandonment and petition are
received by the appropriate officials
more than four weeks prior to the
projected date of publication.
(d) An applicant seeking to abandon
an application filed under 35 U.S.C.
111(a) and § 1.53(b) on or after
December 8, 2004, to obtain a refund of
any search fee paid in the application
must submit a declaration of express
abandonment by way of a petition under
this paragraph in sufficient time to
permit the appropriate officials to
recognize the abandonment before the
application has been taken up for
examination. If a request for refund of
any search fee paid in the application is
not filed with the declaration of express
abandonment under this paragraph or
within two months from the date on
which the declaration of express
abandonment under this paragraph was
filed, the Office may retain the entire
search fee paid in the application. This
two-month period is not extendable. If
a petition and declaration of express
abandonment under this paragraph are
not filed and granted before the
application has been taken up for
examination, the Office will not refund
any part of the search fee paid in the
application except as provided in § 1.26.
Dated: June 15, 2005.
Jon W. Dudas,
Under Secretary of Commerce for Intellectual
Property and Director of the United States
Patent and Trademark Office.
[FR Doc. 05–12198 Filed 6–20–05; 8:45 am]
BILLING CODE 3510–16–P
PART 1—RULES OF PRACTICE IN
PATENT CASES
1. The authority citation for 37 CFR
Part 1 continues to read as follows:
Authority: 35 U.S.C. 2(b)(2).
2. Section 1.138 is amended by
revising paragraph (c) and adding
paragraph (d) to read as follows:
§ 1.138
*
Express abandonment.
*
VerDate jul<14>2003
*
*
*
21:56 Jun 20, 2005
Jkt 205001
PO 00000
Frm 00012
Fmt 4702
Sfmt 4702
35573
DEPARTMENT OF COMMERCE
Patent and Trademark Office
37 CFR Part 1
[Docket No.: 2005–P–062]
RIN 0651–AB91
Acceptance, Processing, Use and
Dissemination of Chemical and ThreeDimensional Biological Structural Data
in Electronic Format
United States Patent and
Trademark Office, Commerce.
ACTION: Advance notice of proposed rule
making.
AGENCY:
SUMMARY: This advance notice of
proposed rule making is to inform the
public that the United States Patent and
Trademark Office (USPTO) is
considering amending its rules of
practice to require submission of
chemical and three-dimensional (3–D)
biological structural data in electronic
format. The USPTO anticipates that
requiring submission of chemical and
3–D biological structural data in
electronic format in patent applications
will improve the processing and
examination of patent applications that
include such data, as well as the
dissemination of such data to searchable
public databases. The purpose of this
notice is to encourage comments on this
topic, in the form of responses to the
questions posed in this notice, from
industry, academia, the patent bars, and
members of the public.
Comment Deadline Date: To be
ensured of consideration, written
comments must be received on or before
August 22, 2005. No public hearing will
be held.
ADDRESSES: Comments should be sent
by electronic mail message over the
Internet addressed to
AB91.Comments@uspto.gov. Comments
may also be submitted by mail
addressed to: Mail Stop Comments—
Patents, Commissioner for Patents, P.O.
Box 1450, Alexandria, VA, 22313–1450,
or by facsimile to (571) 273–3373,
marked to the attention of Lisa J. Hobbs,
Ph.D., Search Systems Project Manager,
Search and Information Resources
Administration, Office of the Deputy
Commissioner for Patent Resources and
Planning. Although comments may be
submitted by mail or facsimile, the
Office prefers to receive comments via
the Internet. If comments are submitted
by mail, the Office prefers that the
comments be submitted on a DOS
formatted 31⁄2 inch disk accompanied by
a paper copy.
E:\FR\FM\21JNP1.SGM
21JNP1
35574
Federal Register / Vol. 70, No. 118 / Tuesday, June 21, 2005 / Proposed Rules
Comments may also be sent by
electronic mail message over the
Internet via the Federal eRulemaking
Portal. See the Federal eRulemaking
Portal Web site (https://
www.regulations.gov) for additional
instructions on providing comments via
the Federal eRulemaking Portal.
The comments will be available for
public inspection at the Office of the
Commissioner for Patents, located in
Madison East, Tenth Floor, 600 Dulany
Street, Alexandria, Virginia, and will be
available through anonymous file
transfer protocol (ftp) via the Internet
(https://www.uspto.gov). Because
comments will be made available for
public inspection, information that the
submitter does not desire to make
public, such as an address or phone
number, should not be included in the
comments.
FOR FURTHER INFORMATION CONTACT: Lisa
J. Hobbs, Ph.D., Search Systems Project
Manager, Search and Information
Resources Administration, Office of the
Deputy Commissioner for Patent
Resources and Planning, by telephone at
(571) 272–3373, respectively, by mail
addressed to: Box Comments—Patents,
Commissioner for Patents, P.O. Box
1450, Alexandria, VA 22313–1450, or by
facsimile to (571) 273–3373, marked to
the attention of Lisa J. Hobbs.
SUPPLEMENTARY INFORMATION:
1. General Background Information: It
is becoming increasingly apparent that
the USPTO needs to begin investigation
of procedures for the submission,
screening, processing, storing,
searching, analysis and dissemination of
chemical and 3–D biological structural
data in appropriate electronic formats.
The rate at which these data are being
generated is poised to increase by
several orders of magnitude in the
coming years as significant advances are
being made in the ability to readily
determine structural information.
Initiatives to fund research in these
areas are being supported by both
numerous governmental agencies and
private industry entities. With the
advancement of capabilities allowed by
automation, the number of public and
private databases hosting these types of
data for information exchange is
growing daily.
It has yet to be determined whether or
not the USPTO will receive an
increasing number of applications
comprising 3–D crystal data and/or
chemical structure data. However, the
USPTO currently receives a significant
amount of chemical structure data, and
has begun to receive some very large
submissions of 3–D protein crystal data.
Consequently, the USPTO has decided
VerDate jul<14>2003
21:56 Jun 20, 2005
Jkt 205001
to begin the planning and coordination
of how best to provide the capability to
manage, process, search, and
disseminate this information as
appropriate.
Similar to the process involved in the
promulgation of the sequence rules (37
CFR 1.821–1.825 and WIPO ST.25), the
USPTO intends to work with other
international intellectual property
offices in developing any new standards
for the submission of chemical or 3–D
structural data in electronic format.
In an effort to facilitate public
comment to the questions set forth
below, the following additional
background information is provided:
2. Background Specific to 3–D
Biological Structural Data: X-ray
crystallographic studies and nuclear
magnetic resonance (NMR) spectroscopy
studies of biological macromolecules
provide mechanisms for obtaining
detailed 3–D structural information. The
current scientific priorities, and
concomitant intellectual property
priorities, of many laboratories include
using 3–D protein crystal data to assist
in unraveling the complex relationship
between sequence, structure, and
function.
Knowledge of the 3–D structures of
biological macromolecules is an
essential element for guiding studies
and developing an understanding of
biological processes. Three dimensional
structural coordinate data provide
essential information that can be
exploited for protein engineering,
rational drug design, and other
biotechnology efforts (Gilliland, et al.
1996 J. Res. Natl. Inst. Stand. Technol.
101: 309–320).
Bioinformatics, the collection and use
of scientific database entries to predict
the structure or behavior or evolutionary
relatedness of particular biological
macromolecules based on sequence
similarity or structural similarity to
known macromolecules, is one of the
fastest growing scientific disciplines.
The ability of the scientific community
to ‘‘data mine’’ known scientific
information is directly dependent on the
public availability of all prior art data.
The worldwide Protein Data Bank
(wwPDB; https://www.wwpdb.org/
index.html) is a collection of all
publicly available 3–D structure data of
large molecules of proteins and nucleic
acids, experimentally determined by Xray crystallography and NMR, which is
freely and publicly available to the
global community. The PDB, which is
under the oversight of the Research
Collaboratory for Structural
Bioinformatics (RCSB, USA), the
Macromolecular Structure Database
(MSD) at the European Bioinformatics
PO 00000
Frm 00013
Fmt 4702
Sfmt 4702
Institute (EBI) and the Protein Data Bank
Japan (PDBj) at the Institute for Protein
Research, has grown from 7 structures
in 1971 to a database containing over
30,900 structures as of May 2005. The
PDB’s growth has been accompanied by
increases in both data content and the
structural complexity of individual
entries. A further acceleration in growth
is anticipated as the result of
developments in high-throughput
structural determination methodologies
and worldwide structural genomics
efforts (Westbrook, et al. 2003 Nucl.
Acids Res. 31(1): 489–491).
There are also many secondary
sources of 3–D protein crystal data and
associated information. One of these is
the Molecular Modeling Database
(MMDB), maintained as part of the
Entrez search system by the National
Center for Biotechnology Information
(NCBI; https://www.ncbi.nlm.nih.gov/),
which is a compilation of all of the PDB
3–D structures of biomolecules and
additionally integrates value-added
chemical, sequence and structural
information in order to facilitate
structure-based homology modeling and
protein structure prediction. The goal of
Entrez’s 3–D-structure database is to
make protein crystal structure
information, and the functional
annotation MMDB adds, easily
accessible to molecular biologists
(Wang, et al. 2002 Nucl. Acids Res.
30(1): 249–252).
All of the major 3–D protein crystal
databases use a variant of the
Crystallographic Information File (CIF)
format as the means for obtaining data
entries with proper annotation. Ratified
in 1990 by the International Union of
Crystallography (ICUr), CIF is a format
that enables the characterization of
small crystal structures. In 1997, the CIF
format was modified to include
information specific to macromolecules,
resulting in version 1.0 of the
macromolecular Crystallographic
Information File (mmCIF) dictionary
(Bourne, et al. 1997 Meth. Enzymol.
227: 571–590). The PDB database
initially accepted files in a proprietary
pdb format in 1971, but has now moved
to accepting all files, and converting the
backfile, into mmCIF. Some databases,
especially those involved in secondary,
value-added information, have further
modified the mmCIF format to include
more data fields and annotations.
MMDB uses the format, ASN.1, which is
specific to the NCBI and addresses
structural and functional linkages. The
ASN.1 format also allows for a 3–D
viewer to be used to visualize the
protein crystal.
In addition to databases containing
information on the crystal structures of
E:\FR\FM\21JNP1.SGM
21JNP1
Federal Register / Vol. 70, No. 118 / Tuesday, June 21, 2005 / Proposed Rules
biomolecules, there are major
repositories for other types of crystal
structures. The Cambridge Structural
Database (CSD), maintained by the
Cambridge Crystallographic Data Centre
(CDCC; https://www.ccdc.cam.ac.uk/), is
a worldwide repository of small
molecule crystal structures and has over
300,000 organic and metallo-organic
compound records. The CSD database
accepts entries in the CIF data format in
plain ASCII text. Repositories for other
types of crystal structures include: the
Nucleic Acids Data Bank (ndb; https://
ndbserver.rutgers.edu/), which stores
oligonucleotides; the Inorganic Crystal
Structure Database (ICSD; https://
www.fiz-informationsdienste.de/en/DB/
icsd/); and, CRYSTMET (https://
www.tothcanada.com/), which stores
metals and alloys.
3. Background Specific to Chemical
Structural Data: While the use of
drawings to denote specific molecular
relationships and chemical bonds is a
very old art, the embodiments and uses
of these drawings are evolving rapidly
as supporting technology evolves. Two
main methods for handling chemical
data are: chemical drawing systems that
depend on annotations added to unique
substance records, in specific electronic
file-types, and text files that are a
compilation of unique data determining
a canonical representation.
Electronic files containing drawings
created by chemical drawing software
would provide the most accessible data
set for processing, use in searching, and
public dissemination. However, there is
currently no single, publicly available,
software that has been accepted as the
standard for this type of drawings. Some
publicly available chemical data
depiction systems are: (1) SMILES
(https://www.daylight.com/dayhtml/
smiles/); (2) SMARTS/SMIRKS (https://
www.daylight.com/dayhtml/doc/theory/
theory.rxn.html#RTFrxn18); (3) ACD
ChemSketch (https://www.acdlabs.com/
download/); and (4) MDL ISIS/Draw
(https://www.mdli.com/downloads/
downloadable/index.jsp). Some
proprietary chemical data depiction
systems are: (1) ChemDraw (https://
www.cambridgesoft.com/products/
family.cfm?FID=2); (2) ACD/Name
(https://www.acdlabs.com/products/
name_lab/); (3) Chemistry 4–D Draw
(https://www.cheminnovation.com/
products/chem4d.asp); and (4)
ChemWindow (https://www.bio-rad.
com/).
One of the difficulties facing the
USPTO in moving toward acceptance of
chemical drawings in electronic format
is the preponderance of proprietary
software and file-types. Prior to filing a
patent application, many applicants
VerDate jul<14>2003
21:56 Jun 20, 2005
Jkt 205001
have already created drawings of
chemical structures of interest for
publication or presentation purposes;
however, these drawings could be in
one of many publicly available filetypes, or in a file-type specific to a
particular software product. It is not
possible to require applicants to
purchase proprietary drawing software,
nor is it possible to accept and handle
all possible file-types.
One alternative to requiring a nonstandard publicly available format,
requiring a proprietary format, or
accepting a multiplicity of drawing filetypes would be the use of a
standardized text format to describe a
chemical structure. Two possibilities for
this type of file are: Chemical Markup
Language (CML; https://www.xmlcml.org/), or a joint effort currently
under way between the International
Union of Pure and Applied Chemistry
and the National Institute of Standards
and Technology, the IUPAC-NIST
Chemical Identifier (INChI; https://
www.iupac.org/projects/2000/2000–
025–1–800.html). A description of INChI
states that it would enable an automatic
conversion to a graphical representation
of a chemical substance that could be
performed anywhere in the world, and
could be built into desktop chemical
structure drawing packages and on-line
chemical structure drawing applets (A.J.
McNaught 2001 https://www.iupac.org/
nomenclature/chem_id_project.html).
Rule Making Considerations
Executive Order 13132: This rule
making does not contain policies with
federalism implications sufficient to
warrant preparation of a Federalism
Assessment under Executive Order
13132 (Aug. 4, 1999).
Executive Order 12866: This rule
making has been determined to be not
significant for purposes of Executive
Order 12866 (Sept. 30, 1993).
Paperwork Reduction Act: This notice
involves information collection
requirements which are subject to
review by the Office of Management and
Budget (OMB) under the Paperwork
Reduction Act of 1995 (44 U.S.C. 3501
et seq.). The collections of information
involved in this notice have been
reviewed and previously approved by
OMB under OMB control numbers:
0651–0022, 0651–0024, 0651–0031, and
0651–0032. The principal impact of the
changes under consideration in this
advance rule would be to revise the
rules of practice to require or provide
for the submission of chemical and
three-dimensional (3–D) biological
structural data in electronic form. The
Office is not resubmitting any
information collection package to OMB
PO 00000
Frm 00014
Fmt 4702
Sfmt 4702
35575
for its review and approval because the
this advance notice does not propose
any changes that would affect the
information collection requirements
associated with the information
collection under these OMB control
numbers. If the Office proceeds with
proposing changes to the rules of
practice relating to the submission of
chemical and three-dimensional (3–D)
biological structural data in electronic
form, the Office will resubmit an
information collection package to OMB
for its review and approval for any
collections of information whose
requirements will be revised as a result
of the proposed rule changes.
Interested persons are requested to
send comments regarding these
information collections, including
suggestions for reducing this burden, to
Robert J. Spar, Director, Office of Patent
Legal Administration, Commissioner for
Patents, P.O. Box 1450, Alexandria, VA
22313–1450, or to the Office of
Information and Regulatory Affairs,
Office of Management and Budget, New
Executive Office Building, Room 10235,
725 17th Street, N.W., Washington, D.C.
20503, Attention: Desk Officer for the
Patent and Trademark Office.
Notwithstanding any other provision
of law, no person is required to respond
to nor shall a person be subject to a
penalty for failure to comply with a
collection of information subject to the
requirements of the Paperwork
Reduction Act unless that collection of
information displays a currently valid
OMB control number.
4. Comments on the following
Questions and Any Other Related
Matters Are Solicited:
A. Questions Pertaining to the Creation
of 3–D Structural Data Files
1. What benefits do you foresee for the
applicant if electronic filing is adopted?
What disadvantages do you foresee?
2. What types of 3–D data would be
best submitted electronically?
Examples:
• Small organic crystals.
• Macromolecular peptide/protein
crystals.
• Inorganic crystals.
• Metallic crystals.
• Other.
3. Should electronic submission of 3–
D data be mandatory, optional, or
mandatory for some types (e.g., protein
crystals) and optional for others (e.g.,
small organic crystals)?
4. If electronic submission is
mandatory, should the USPTO require
all 3–D information cited in application
to be submitted in electronic format,
including prior art, or only new data?
E:\FR\FM\21JNP1.SGM
21JNP1
35576
Federal Register / Vol. 70, No. 118 / Tuesday, June 21, 2005 / Proposed Rules
5. Have tables of 3–D data generally
been created for other purposes before
preparation of a patent application, e.g.,
for publication in a scientific journal or
submission to a database? If so,
• What format(s) are used (e.g.,
mmCIF, pdb, CIF, other)?
• What authoring tool is used to
create the files, e.g., ADIT https://
pdb.rutgers.edu/mmcif/ADIT/
index.html?
• What software, if any, is used to
validate files of 3–D data, e.g., ADIT
Validation Tool or enCIFer (https://
www.ccdc.cam.ac.uk/free_services/
encifer/)?
6. Have most of the 3–D tables been
submitted to a database before inclusion
in a patent application? If so, which
one? Examples:
• https://www.ccdc.cam.ac.uk/
products/csd/
• https://www.rcsb.org/pdb/
• https://www.fizinformationsdienste.de/en/DB/icsd/
• https://www.tothcanada.com/
7. Have most of the 3–D tables been
published before inclusion in a patent
application?
8. Database providers require certain
annotation data. Would any of the
annotation data currently required by 3–
D database providers be unknown or
proprietary at the time of filing a patent
application (e.g., method used for
crystal creation)?
9. Database providers often establish a
controlled vocabulary for annotation or
feature description information. Would
there be any problems created during
patent application prosecution if the
electronic file relied on dynamic
controlled dictionaries or vocabularies,
controlled and maintained by database
providers, not the USPTO, for the
description of features, etc. What would
be the pros and cons if the USPTO were
to incorporate by reference a public
database controlled vocabulary into any
adopted standard? Examples:
• https://pdb.rutgers.edu/
cc_dict_tut.html
• https://ndbserver.rutgers.edu/mmcif/
dictionaries/
10. Is there annotation data specific to
a patent application that does not
appear in public database files but that
would be desirable to provide for an
electronic submission in a patent
application (e.g., continuing application
data, attorney’s docket number)?
11. Do many/most file wrapper
submissions with 3–D data contain
multiple 3–D tables?
B. Questions Pertaining to the USPTO
Receipt of 3–D Files
1. In general, 3–D structure data tables
submitted as part of a patent application
VerDate jul<14>2003
21:56 Jun 20, 2005
Jkt 205001
are quite lengthy. Should the USPTO
require that all 3–D files greater than a
certain size be submitted in electronic
media only?
2. Should the USPTO require
submission in electronic format at the
time of filing, or, if a paper copy is filed,
permit the electronic submission to be
filed later (with a statement indicating
that the electronic version is the same
as the version originally filed)?
3. Should any statement that comes
with an electronic file outline the
authoring tool and certify the use of a
validation tool?
4. Should the rules be revised to
specify that 3–D biological structural
data, if a paper copy is provided, is to
appear in a special section, e.g., between
the specification and the Sequence
Listing?
C. Questions Pertaining to the Use of 3–
D Electronic Files by the USPTO
Examiners/STIC Personnel
1. If enough patent applications are
filed directed to 3–D structures to go
forward with pursuing search capability
(a 3–D file search, not the standard
sequence search and text search already
performed) of some sort, what databases
should be investigated?
2. What software viewer would be
recommended for visual interpretation
of the text tables? Examples:
• https://www.ncbi.nlm.nih.gov/
Structure/CN3–D/cn3–D.shtml
• https://products.cambridgesoft.com/
ProdInfo.cfm?pid=285
• https://www.proteinscope.com/
• https://www.candomultimedia.com/
medical/
D. Questions Pertaining to 3–D File
Export to a Public Database Partner
1. If the USPTO receives 3–D
structural data in electronic form, the
USPTO would likely be able to export
the data to a searchable public database
upon publication of the application or
patent grant. What databases should be
investigated for a USPTO export
arrangement?
2. Would public databases be willing
to work with the USPTO in developing
acceptable formats and annotations, if
that would be the best submission
practice for applicants?
E. Questions Pertaining to the USPTO
Publication of 3–D Files
1. Should all 3–D files be posted on
the USPTO’s Publication Site for Issued
and Published Sequences (PSIPS;
https://seqdata.uspto.gov/)?
2. Should the files be part of the text
or image of the patent application
publication or patent grant aside from
electronic posting on PSIPS?
PO 00000
Frm 00015
Fmt 4702
Sfmt 4702
F. Question Pertaining to 3–D File
Export to the USPTO Customers
The USPTO would be exporting in a
new file-type; would this have an
adverse or beneficial impact on the
USPTO customers?
G. Questions Pertaining to the Creation
of Chemistry Structural Data Files
1. What benefits do you foresee for the
applicant if electronic filing is adopted?
What disadvantages do you foresee?
2. Has a structural chemistry data file
or drawing generally been created for
other purposes before preparation of a
patent application, e.g., for publication
in a scientific journal or submission to
a database? If so, in what format: .mol,
.cdx, CML, INChI, other?
3. If drawing tools are used by
applicants, which tools are generally
used to create the files, e.g., ChemDraw,
ISIS/Draw, ACD/Name?
• https://www.cambridgesoft.com/
products/family.cfm?FID=2
• https://www.mdli.com/products/
framework/isis_draw/index.jsp
• https://www.acdlabs.com/products/
name_lab/name/
4. Is there annotation data that should
be added to the drawings? What
annotations? How would applicants
prefer to add additional data?
5. Possibly applicants want to cite
inventors, attorneys, continuing
application data, attorney’s docket
number, etc.?
6. Should the USPTO require all
structures cited in a patent application
be submitted in electronic format? Only
new data (not prior art)? Only a
representative drawing? Only the
‘‘actual invention’’ after restriction of
the claims and election of an invention?
7. Would a single representation be
deemed a limitation to applicant’s
disclosure?
8. Do many/most file wrapper
submissions with chemical structures
contain multiple chemical structure
drawings?
9. Have any chemical drawings
generally been submitted to a public
entity (e.g., a database or journal) before
the filing of a patent application?
10. Have most of the drawings been
published before the filing of a patent
application?
11. Would it be a hardship for
applicants if the USPTO required
drawings in a proprietary software
format?
12. Would it be a hardship for
applicants if the USPTO required
drawings in a text format that is not yet
supported by the major drawing
software tools?
• How well known is the CML
format?
E:\FR\FM\21JNP1.SGM
21JNP1
Federal Register / Vol. 70, No. 118 / Tuesday, June 21, 2005 / Proposed Rules
I https://www.xml-cml.org/
• How well known is the INChI
format?
I https://www.iupac.org/publications/
ci/2001/may/project_2000–025–1–
050.html
I https://www.iupac.org/projects/
2000/2000–025–1–800.html#clip
13. What is the state of the art for
chemical drawings?
I https://www.iupac.org/publications/
ci/2002/2404/XML.html
H. Questions Pertaining to the USPTO
Receipt of Chemistry Structure Files
1. Chemical structure data received by
the USPTO varies widely in size.
Should the USPTO require that all
chemical structure files greater than a
certain size be submitted in electronic
media only?
2. Should the USPTO require
submission in electronic format at the
time of filing, or, if a paper copy is filed,
permit the electronic submission to be
filed later (with a statement indicating
that the electronic version is the same
as the version originally filed)?
3. Should the rules be revised to
specify that chemical structure data, if
a paper copy is supplied, is to appear in
a special section, e.g., between the
specification and the Sequence Listing,
or as part of the drawings?
4. Chemical structures are often
presented in the specification and
claims in Markush format wherein a
basic structure is defined, but portions
thereof are variable. Are there drawing
tools available that accurately render
these types of structures? If not, what
approach should the USPTO take to
ensure that the data submitted
appropriately reflects the invention
described or claimed in the patent
application. For example, the USPTO
could require: An ‘‘exemplary’’ drawing
at the time of filing; a drawing at the
time of a restriction election, e.g., a
single embodiment of a Markush claim;
or, possibly multiple drawings.
5. The USPTO needs to have certain
data associated with files. Since there is
no annotation data in chemical drawing
files, should the USPTO require a ‘‘read
me’’ text file to accompany the drawing
file? Should the title of the file be the
name of the drawing?
be problematic, how can the USPTO
effectively require submission of a
representative drawing to be searched
and, possibly, published?
J. Questions Pertaining to Chemistry
Structure File Export to a Public
Database Partner
1. Should the USPTO send chemical
structure data files to a public database
partner? If so, which one(s)?
2. Should the USPTO export data to
CAS for inclusion in the Registry file?
What about other private providers?
• https://www.cas.org/EO/regsys.html
K. Question Pertaining to the USPTO
Publication of Chemistry Structure Files
1. Should all chemistry structure files
be posted on the USPTO’s Publication
Site for Issued and Published Sequences
(PSIPS; https://seqdata.uspto.gov/), or
should the chemistry drawing be
published with the TIFF images of the
patent application publication or patent
grant?
L. Question Pertaining to Chemistry
Structure File Export to the USPTO
Customers
1. Should we change the drawing files
that are sent to the USPTO customers?
• Currently, .cdx, .mol, and TIFF
versions are present (Note: common to
Patent and Trademark Applications)
Dated: June 15, 2005.
Jon W. Dudas,
Under Secretary of Commerce for Intellectual
Property and Director of the United States
Patent and Trademark Office.
[FR Doc. 05–12199 Filed 6–20–05; 8:45 am]
BILLING CODE 3510–16–P
DEPARTMENT OF HOMELAND
SECURITY
Federal Emergency Management
Agency
44 CFR Part 67
[Docket No. FEMA–D–7622]
Proposed Flood Elevation
Determinations
I. Question Pertaining to the Use of
Chemistry Structure Files by the USPTO
Examiners/STIC Personnel
Federal Emergency
Management Agency (FEMA),
Emergency Preparedness and Response
Directorate, Department of Homeland
Security.
ACTION: Proposed rule.
If a chemical structure drawing were
required at the time of filing, how often
might it have so many variables (that
may be subject to a restriction/election
requirement) that it cannot be
effectively searched? If this is likely to
SUMMARY: Technical information or
comments are requested on the
proposed Base (1% annual chance)
Flood Elevations (BFEs) and proposed
BFE modifications for the communities
listed below. The BFEs are the basis for
VerDate jul<14>2003
22:25 Jun 20, 2005
Jkt 205001
AGENCY:
PO 00000
Frm 00016
Fmt 4702
Sfmt 4702
35577
the floodplain management measures
that the community is required either to
adopt or to show evidence of being
already in effect in order to qualify or
remain qualified for participation in the
National Flood Insurance Program
(NFIP).
The comment period is ninety
(90) days following the second
publication of this proposed rule in a
newspaper of local circulation in each
community.
DATES:
The proposed BFEs for each
community are available for inspection
at the office of the Chief Executive
Officer of each community. The
respective addresses are listed in the
table below.
FOR FURTHER INFORMATION CONTACT:
Doug Bellomo, P.E., Hazard
Identification Section, Emergency
Preparedness and Response Directorate,
FEMA, 500 C Street SW., Washington,
DC 20472, (202) 646–2903.
SUPPLEMENTARY INFORMATION: FEMA
proposes to make determinations of
BFEs and modified BFEs for each
community listed below, in accordance
with section 110 of the Flood Disaster
Protection Act of 1973, 42 U.S.C. 4104,
and 44 CFR 67.4(a).
These proposed base flood elevations
and modified BFEs, together with the
floodplain management criteria required
by 44 CFR 60.3, are the minimum that
are required. They should not be
construed to mean that the community
must change any existing ordinances
that are more stringent in their
floodplain management requirements.
The community may at any time enact
stricter requirements of its own, or
pursuant to policies established by other
Federal, state or regional entities. These
proposed elevations are used to meet
the floodplain management
requirements of the NFIP and are also
used to calculate the appropriate flood
insurance premium rates for new
buildings built after these elevations are
made final, and for the contents in these
buildings.
National Environmental Policy Act.
This proposed rule is categorically
excluded from the requirements of 44
CFR part 10, Environmental
Consideration. No environmental
impact assessment has been prepared.
Regulatory Flexibility Act. The
Mitigation Division Director of the
Emergency Preparedness and Response
Directorate certifies that this proposed
rule is exempt from the requirements of
the Regulatory Flexibility Act because
proposed or modified BFEs are required
by the Flood Disaster Protection Act of
1973, 42 U.S.C. 4105, and are required
ADDRESSES:
E:\FR\FM\21JNP1.SGM
21JNP1
]]>Agencies
[Federal Register Volume 70, Number 118 (Tuesday, June 21, 2005)]
[Proposed Rules]
[Pages 35573-35577]
From the Federal Register Online via the Government Printing Office [www.gpo.gov]
[FR Doc No: 05-12199]
-----------------------------------------------------------------------
DEPARTMENT OF COMMERCE
Patent and Trademark Office
37 CFR Part 1
[Docket No.: 2005-P-062]
RIN 0651-AB91
Acceptance, Processing, Use and Dissemination of Chemical and
Three-Dimensional Biological Structural Data in Electronic Format
AGENCY: United States Patent and Trademark Office, Commerce.
ACTION: Advance notice of proposed rule making.
-----------------------------------------------------------------------
SUMMARY: This advance notice of proposed rule making is to inform the
public that the United States Patent and Trademark Office (USPTO) is
considering amending its rules of practice to require submission of
chemical and three-dimensional (3-D) biological structural data in
electronic format. The USPTO anticipates that requiring submission of
chemical and 3-D biological structural data in electronic format in
patent applications will improve the processing and examination of
patent applications that include such data, as well as the
dissemination of such data to searchable public databases. The purpose
of this notice is to encourage comments on this topic, in the form of
responses to the questions posed in this notice, from industry,
academia, the patent bars, and members of the public.
Comment Deadline Date: To be ensured of consideration, written
comments must be received on or before August 22, 2005. No public
hearing will be held.
ADDRESSES: Comments should be sent by electronic mail message over the
Internet addressed to AB91.Comments@uspto.gov. Comments may also be
submitted by mail addressed to: Mail Stop Comments--Patents,
Commissioner for Patents, P.O. Box 1450, Alexandria, VA, 22313-1450, or
by facsimile to (571) 273-3373, marked to the attention of Lisa J.
Hobbs, Ph.D., Search Systems Project Manager, Search and Information
Resources Administration, Office of the Deputy Commissioner for Patent
Resources and Planning. Although comments may be submitted by mail or
facsimile, the Office prefers to receive comments via the Internet. If
comments are submitted by mail, the Office prefers that the comments be
submitted on a DOS formatted 3\1/2\ inch disk accompanied by a paper
copy.
[[Page 35574]]
Comments may also be sent by electronic mail message over the
Internet via the Federal eRulemaking Portal. See the Federal
eRulemaking Portal Web site (https://www.regulations.gov) for additional
instructions on providing comments via the Federal eRulemaking Portal.
The comments will be available for public inspection at the Office
of the Commissioner for Patents, located in Madison East, Tenth Floor,
600 Dulany Street, Alexandria, Virginia, and will be available through
anonymous file transfer protocol (ftp) via the Internet (https://
www.uspto.gov). Because comments will be made available for public
inspection, information that the submitter does not desire to make
public, such as an address or phone number, should not be included in
the comments.
FOR FURTHER INFORMATION CONTACT: Lisa J. Hobbs, Ph.D., Search Systems
Project Manager, Search and Information Resources Administration,
Office of the Deputy Commissioner for Patent Resources and Planning, by
telephone at (571) 272-3373, respectively, by mail addressed to: Box
Comments--Patents, Commissioner for Patents, P.O. Box 1450, Alexandria,
VA 22313-1450, or by facsimile to (571) 273-3373, marked to the
attention of Lisa J. Hobbs.
SUPPLEMENTARY INFORMATION:
1. General Background Information: It is becoming increasingly
apparent that the USPTO needs to begin investigation of procedures for
the submission, screening, processing, storing, searching, analysis and
dissemination of chemical and 3-D biological structural data in
appropriate electronic formats. The rate at which these data are being
generated is poised to increase by several orders of magnitude in the
coming years as significant advances are being made in the ability to
readily determine structural information. Initiatives to fund research
in these areas are being supported by both numerous governmental
agencies and private industry entities. With the advancement of
capabilities allowed by automation, the number of public and private
databases hosting these types of data for information exchange is
growing daily.
It has yet to be determined whether or not the USPTO will receive
an increasing number of applications comprising 3-D crystal data and/or
chemical structure data. However, the USPTO currently receives a
significant amount of chemical structure data, and has begun to receive
some very large submissions of 3-D protein crystal data. Consequently,
the USPTO has decided to begin the planning and coordination of how
best to provide the capability to manage, process, search, and
disseminate this information as appropriate.
Similar to the process involved in the promulgation of the sequence
rules (37 CFR 1.821-1.825 and WIPO ST.25), the USPTO intends to work
with other international intellectual property offices in developing
any new standards for the submission of chemical or 3-D structural data
in electronic format.
In an effort to facilitate public comment to the questions set
forth below, the following additional background information is
provided:
2. Background Specific to 3-D Biological Structural Data: X-ray
crystallographic studies and nuclear magnetic resonance (NMR)
spectroscopy studies of biological macromolecules provide mechanisms
for obtaining detailed 3-D structural information. The current
scientific priorities, and concomitant intellectual property
priorities, of many laboratories include using 3-D protein crystal data
to assist in unraveling the complex relationship between sequence,
structure, and function.
Knowledge of the 3-D structures of biological macromolecules is an
essential element for guiding studies and developing an understanding
of biological processes. Three dimensional structural coordinate data
provide essential information that can be exploited for protein
engineering, rational drug design, and other biotechnology efforts
(Gilliland, et al. 1996 J. Res. Natl. Inst. Stand. Technol. 101: 309-
320).
Bioinformatics, the collection and use of scientific database
entries to predict the structure or behavior or evolutionary
relatedness of particular biological macromolecules based on sequence
similarity or structural similarity to known macromolecules, is one of
the fastest growing scientific disciplines. The ability of the
scientific community to ``data mine'' known scientific information is
directly dependent on the public availability of all prior art data.
The worldwide Protein Data Bank (wwPDB; https://www.wwpdb.org/
index.html) is a collection of all publicly available 3-D structure
data of large molecules of proteins and nucleic acids, experimentally
determined by X-ray crystallography and NMR, which is freely and
publicly available to the global community. The PDB, which is under the
oversight of the Research Collaboratory for Structural Bioinformatics
(RCSB, USA), the Macromolecular Structure Database (MSD) at the
European Bioinformatics Institute (EBI) and the Protein Data Bank Japan
(PDBj) at the Institute for Protein Research, has grown from 7
structures in 1971 to a database containing over 30,900 structures as
of May 2005. The PDB's growth has been accompanied by increases in both
data content and the structural complexity of individual entries. A
further acceleration in growth is anticipated as the result of
developments in high-throughput structural determination methodologies
and worldwide structural genomics efforts (Westbrook, et al. 2003 Nucl.
Acids Res. 31(1): 489-491).
There are also many secondary sources of 3-D protein crystal data
and associated information. One of these is the Molecular Modeling
Database (MMDB), maintained as part of the Entrez search system by the
National Center for Biotechnology Information (NCBI; https://
www.ncbi.nlm.nih.gov/), which is a compilation of all of the PDB 3-D
structures of biomolecules and additionally integrates value-added
chemical, sequence and structural information in order to facilitate
structure-based homology modeling and protein structure prediction. The
goal of Entrez's 3-D-structure database is to make protein crystal
structure information, and the functional annotation MMDB adds, easily
accessible to molecular biologists (Wang, et al. 2002 Nucl. Acids Res.
30(1): 249-252).
All of the major 3-D protein crystal databases use a variant of the
Crystallographic Information File (CIF) format as the means for
obtaining data entries with proper annotation. Ratified in 1990 by the
International Union of Crystallography (ICUr), CIF is a format that
enables the characterization of small crystal structures. In 1997, the
CIF format was modified to include information specific to
macromolecules, resulting in version 1.0 of the macromolecular
Crystallographic Information File (mmCIF) dictionary (Bourne, et al.
1997 Meth. Enzymol. 227: 571-590). The PDB database initially accepted
files in a proprietary pdb format in 1971, but has now moved to
accepting all files, and converting the backfile, into mmCIF. Some
databases, especially those involved in secondary, value-added
information, have further modified the mmCIF format to include more
data fields and annotations. MMDB uses the format, ASN.1, which is
specific to the NCBI and addresses structural and functional linkages.
The ASN.1 format also allows for a 3-D viewer to be used to visualize
the protein crystal.
In addition to databases containing information on the crystal
structures of
[[Page 35575]]
biomolecules, there are major repositories for other types of crystal
structures. The Cambridge Structural Database (CSD), maintained by the
Cambridge Crystallographic Data Centre (CDCC; https://
www.ccdc.cam.ac.uk/), is a worldwide repository of small molecule
crystal structures and has over 300,000 organic and metallo-organic
compound records. The CSD database accepts entries in the CIF data
format in plain ASCII text. Repositories for other types of crystal
structures include: the Nucleic Acids Data Bank (ndb; https://
ndbserver.rutgers.edu/), which stores oligonucleotides; the Inorganic
Crystal Structure Database ( ICSD; https://www.fiz-
informationsdienste.de/en/DB/icsd/); and, CRYSTMET [reg] (https://
www.tothcanada.com/), which stores metals and alloys.
3. Background Specific to Chemical Structural Data: While the use
of drawings to denote specific molecular relationships and chemical
bonds is a very old art, the embodiments and uses of these drawings are
evolving rapidly as supporting technology evolves. Two main methods for
handling chemical data are: chemical drawing systems that depend on
annotations added to unique substance records, in specific electronic
file-types, and text files that are a compilation of unique data
determining a canonical representation.
Electronic files containing drawings created by chemical drawing
software would provide the most accessible data set for processing, use
in searching, and public dissemination. However, there is currently no
single, publicly available, software that has been accepted as the
standard for this type of drawings. Some publicly available chemical
data depiction systems are: (1) SMILES (https://www.daylight.com/
dayhtml/smiles/); (2) SMARTS/SMIRKS (https://www.daylight.com/dayhtml/
doc/theory/theory.rxn.html#RTFrxn18); (3) ACD ChemSketch (https://
www.acdlabs.com/download/); and (4) MDL ISIS/Draw (https://www.mdli.com/
downloads/downloadable/index.jsp). Some proprietary chemical data
depiction systems are: (1) ChemDraw (https://www.cambridgesoft.com/
products/family.cfm?FID=2); (2) ACD/Name (https://www.acdlabs.com/
products/name_lab/); (3) Chemistry 4-D Draw (https://
www.cheminnovation.com/products/chem4d.asp); and (4) ChemWindow (http:/
/www.bio-rad. com/).
One of the difficulties facing the USPTO in moving toward
acceptance of chemical drawings in electronic format is the
preponderance of proprietary software and file-types. Prior to filing a
patent application, many applicants have already created drawings of
chemical structures of interest for publication or presentation
purposes; however, these drawings could be in one of many publicly
available file-types, or in a file-type specific to a particular
software product. It is not possible to require applicants to purchase
proprietary drawing software, nor is it possible to accept and handle
all possible file-types.
One alternative to requiring a non-standard publicly available
format, requiring a proprietary format, or accepting a multiplicity of
drawing file-types would be the use of a standardized text format to
describe a chemical structure. Two possibilities for this type of file
are: Chemical Markup Language (CML; https://www.xml-cml.org/), or a
joint effort currently under way between the International Union of
Pure and Applied Chemistry and the National Institute of Standards and
Technology, the IUPAC-NIST Chemical Identifier (INChI; https://
www.iupac.org/projects/2000/2000-025-1-800.html). A description of
INChI states that it would enable an automatic conversion to a
graphical representation of a chemical substance that could be
performed anywhere in the world, and could be built into desktop
chemical structure drawing packages and on-line chemical structure
drawing applets (A.J. McNaught 2001 https://www.iupac.org/nomenclature/
chem_id_project.html).
Rule Making Considerations
Executive Order 13132: This rule making does not contain policies
with federalism implications sufficient to warrant preparation of a
Federalism Assessment under Executive Order 13132 (Aug. 4, 1999).
Executive Order 12866: This rule making has been determined to be
not significant for purposes of Executive Order 12866 (Sept. 30, 1993).
Paperwork Reduction Act: This notice involves information
collection requirements which are subject to review by the Office of
Management and Budget (OMB) under the Paperwork Reduction Act of 1995
(44 U.S.C. 3501 et seq.). The collections of information involved in
this notice have been reviewed and previously approved by OMB under OMB
control numbers: 0651-0022, 0651-0024, 0651-0031, and 0651-0032. The
principal impact of the changes under consideration in this advance
rule would be to revise the rules of practice to require or provide for
the submission of chemical and three-dimensional (3-D) biological
structural data in electronic form. The Office is not resubmitting any
information collection package to OMB for its review and approval
because the this advance notice does not propose any changes that would
affect the information collection requirements associated with the
information collection under these OMB control numbers. If the Office
proceeds with proposing changes to the rules of practice relating to
the submission of chemical and three-dimensional (3-D) biological
structural data in electronic form, the Office will resubmit an
information collection package to OMB for its review and approval for
any collections of information whose requirements will be revised as a
result of the proposed rule changes.
Interested persons are requested to send comments regarding these
information collections, including suggestions for reducing this
burden, to Robert J. Spar, Director, Office of Patent Legal
Administration, Commissioner for Patents, P.O. Box 1450, Alexandria, VA
22313-1450, or to the Office of Information and Regulatory Affairs,
Office of Management and Budget, New Executive Office Building, Room
10235, 725 17th Street, N.W., Washington, D.C. 20503, Attention: Desk
Officer for the Patent and Trademark Office.
Notwithstanding any other provision of law, no person is required
to respond to nor shall a person be subject to a penalty for failure to
comply with a collection of information subject to the requirements of
the Paperwork Reduction Act unless that collection of information
displays a currently valid OMB control number.
4. Comments on the following Questions and Any Other Related
Matters Are Solicited:
A. Questions Pertaining to the Creation of 3-D Structural Data Files
1. What benefits do you foresee for the applicant if electronic
filing is adopted? What disadvantages do you foresee?
2. What types of 3-D data would be best submitted electronically?
Examples:
Small organic crystals.
Macromolecular peptide/protein crystals.
Inorganic crystals.
Metallic crystals.
Other.
3. Should electronic submission of 3-D data be mandatory, optional,
or mandatory for some types (e.g., protein crystals) and optional for
others (e.g., small organic crystals)?
4. If electronic submission is mandatory, should the USPTO require
all 3-D information cited in application to be submitted in electronic
format, including prior art, or only new data?
[[Page 35576]]
5. Have tables of 3-D data generally been created for other
purposes before preparation of a patent application, e.g., for
publication in a scientific journal or submission to a database? If so,
What format(s) are used (e.g., mmCIF, pdb, CIF, other)?
What authoring tool is used to create the files, e.g.,
ADIT https://pdb.rutgers.edu/mmcif/ADIT/?
What software, if any, is used to validate files of 3-D
data, e.g., ADIT Validation Tool or enCIFer (https://www.ccdc.cam.ac.uk/
free_services/encifer/)?
6. Have most of the 3-D tables been submitted to a database before
inclusion in a patent application? If so, which one? Examples:
https://www.ccdc.cam.ac.uk/products/csd/
https://www.rcsb.org/pdb/
https://www.fiz-informationsdienste.de/en/DB/icsd/
https://www.tothcanada.com/
7. Have most of the 3-D tables been published before inclusion in a
patent application?
8. Database providers require certain annotation data. Would any of
the annotation data currently required by 3-D database providers be
unknown or proprietary at the time of filing a patent application
(e.g., method used for crystal creation)?
9. Database providers often establish a controlled vocabulary for
annotation or feature description information. Would there be any
problems created during patent application prosecution if the
electronic file relied on dynamic controlled dictionaries or
vocabularies, controlled and maintained by database providers, not the
USPTO, for the description of features, etc. What would be the pros and
cons if the USPTO were to incorporate by reference a public database
controlled vocabulary into any adopted standard? Examples:
https://pdb.rutgers.edu/cc_dict_tut.html
https://ndbserver.rutgers.edu/mmcif/dictionaries/
10. Is there annotation data specific to a patent application that
does not appear in public database files but that would be desirable to
provide for an electronic submission in a patent application (e.g.,
continuing application data, attorney's docket number)?
11. Do many/most file wrapper submissions with 3-D data contain
multiple 3-D tables?
B. Questions Pertaining to the USPTO Receipt of 3-D Files
1. In general, 3-D structure data tables submitted as part of a
patent application are quite lengthy. Should the USPTO require that all
3-D files greater than a certain size be submitted in electronic media
only?
2. Should the USPTO require submission in electronic format at the
time of filing, or, if a paper copy is filed, permit the electronic
submission to be filed later (with a statement indicating that the
electronic version is the same as the version originally filed)?
3. Should any statement that comes with an electronic file outline
the authoring tool and certify the use of a validation tool?
4. Should the rules be revised to specify that 3-D biological
structural data, if a paper copy is provided, is to appear in a special
section, e.g., between the specification and the Sequence Listing?
C. Questions Pertaining to the Use of 3-D Electronic Files by the USPTO
Examiners/STIC Personnel
1. If enough patent applications are filed directed to 3-D
structures to go forward with pursuing search capability (a 3-D file
search, not the standard sequence search and text search already
performed) of some sort, what databases should be investigated?
2. What software viewer would be recommended for visual
interpretation of the text tables? Examples:
https://www.ncbi.nlm.nih.gov/Structure/CN3-D/cn3-D.shtml
https://products.cambridgesoft.com/ProdInfo.cfm?pid=285
https://www.proteinscope.com/
https://www.candomultimedia.com/medical/
D. Questions Pertaining to 3-D File Export to a Public Database Partner
1. If the USPTO receives 3-D structural data in electronic form,
the USPTO would likely be able to export the data to a searchable
public database upon publication of the application or patent grant.
What databases should be investigated for a USPTO export arrangement?
2. Would public databases be willing to work with the USPTO in
developing acceptable formats and annotations, if that would be the
best submission practice for applicants?
E. Questions Pertaining to the USPTO Publication of 3-D Files
1. Should all 3-D files be posted on the USPTO's Publication Site
for Issued and Published Sequences (PSIPS; https://seqdata.uspto.gov/)?
2. Should the files be part of the text or image of the patent
application publication or patent grant aside from electronic posting
on PSIPS?
F. Question Pertaining to 3-D File Export to the USPTO Customers
The USPTO would be exporting in a new file-type; would this have an
adverse or beneficial impact on the USPTO customers?
G. Questions Pertaining to the Creation of Chemistry Structural Data
Files
1. What benefits do you foresee for the applicant if electronic
filing is adopted? What disadvantages do you foresee?
2. Has a structural chemistry data file or drawing generally been
created for other purposes before preparation of a patent application,
e.g., for publication in a scientific journal or submission to a
database? If so, in what format: .mol, .cdx, CML, INChI, other?
3. If drawing tools are used by applicants, which tools are
generally used to create the files, e.g., ChemDraw, ISIS/Draw, ACD/
Name?
https://www.cambridgesoft.com/products/family.cfm?FID=2
https://www.mdli.com/products/framework/isis_draw/
index.jsp
https://www.acdlabs.com/products/name_lab/name/
4. Is there annotation data that should be added to the drawings?
What annotations? How would applicants prefer to add additional data?
5. Possibly applicants want to cite inventors, attorneys,
continuing application data, attorney's docket number, etc.?
6. Should the USPTO require all structures cited in a patent
application be submitted in electronic format? Only new data (not prior
art)? Only a representative drawing? Only the ``actual invention''
after restriction of the claims and election of an invention?
7. Would a single representation be deemed a limitation to
applicant's disclosure?
8. Do many/most file wrapper submissions with chemical structures
contain multiple chemical structure drawings?
9. Have any chemical drawings generally been submitted to a public
entity (e.g., a database or journal) before the filing of a patent
application?
10. Have most of the drawings been published before the filing of a
patent application?
11. Would it be a hardship for applicants if the USPTO required
drawings in a proprietary software format?
12. Would it be a hardship for applicants if the USPTO required
drawings in a text format that is not yet supported by the major
drawing software tools?
How well known is the CML format?
[[Page 35577]]
[s] https://www.xml-cml.org/
How well known is the INChI format?
[s] https://www.iupac.org/publications/ci/
2001/may/project_2000-025-1-050.html
[s] https://www.iupac.org/projects/2000/
2000-025-1-800.html#clip
13. What is the state of the art for chemical drawings?
[s] https://www.iupac.org/publications/ci/
2002/2404/XML.html
H. Questions Pertaining to the USPTO Receipt of Chemistry Structure
Files
1. Chemical structure data received by the USPTO varies widely in
size. Should the USPTO require that all chemical structure files
greater than a certain size be submitted in electronic media only?
2. Should the USPTO require submission in electronic format at the
time of filing, or, if a paper copy is filed, permit the electronic
submission to be filed later (with a statement indicating that the
electronic version is the same as the version originally filed)?
3. Should the rules be revised to specify that chemical structure
data, if a paper copy is supplied, is to appear in a special section,
e.g., between the specification and the Sequence Listing, or as part of
the drawings?
4. Chemical structures are often presented in the specification and
claims in Markush format wherein a basic structure is defined, but
portions thereof are variable. Are there drawing tools available that
accurately render these types of structures? If not, what approach
should the USPTO take to ensure that the data submitted appropriately
reflects the invention described or claimed in the patent application.
For example, the USPTO could require: An ``exemplary'' drawing at the
time of filing; a drawing at the time of a restriction election, e.g.,
a single embodiment of a Markush claim; or, possibly multiple drawings.
5. The USPTO needs to have certain data associated with files.
Since there is no annotation data in chemical drawing files, should the
USPTO require a ``read me'' text file to accompany the drawing file?
Should the title of the file be the name of the drawing?
I. Question Pertaining to the Use of Chemistry Structure Files by the
USPTO Examiners/STIC Personnel
If a chemical structure drawing were required at the time of
filing, how often might it have so many variables (that may be subject
to a restriction/election requirement) that it cannot be effectively
searched? If this is likely to be problematic, how can the USPTO
effectively require submission of a representative drawing to be
searched and, possibly, published?
J. Questions Pertaining to Chemistry Structure File Export to a Public
Database Partner
1. Should the USPTO send chemical structure data files to a public
database partner? If so, which one(s)?
2. Should the USPTO export data to CAS for inclusion in the
Registry file? What about other private providers?
https://www.cas.org/EO/regsys.html
K. Question Pertaining to the USPTO Publication of Chemistry Structure
Files
1. Should all chemistry structure files be posted on the USPTO's
Publication Site for Issued and Published Sequences (PSIPS; https://
seqdata.uspto.gov/), or should the chemistry drawing be published with
the TIFF images of the patent application publication or patent grant?
L. Question Pertaining to Chemistry Structure File Export to the USPTO
Customers
1. Should we change the drawing files that are sent to the USPTO
customers?
Currently, .cdx, .mol, and TIFF versions are present
(Note: common to Patent and Trademark Applications)
Dated: June 15, 2005.
Jon W. Dudas,
Under Secretary of Commerce for Intellectual Property and Director of
the United States Patent and Trademark Office.
[FR Doc. 05-12199 Filed 6-20-05; 8:45 am]
BILLING CODE 3510-16-P
