[Federal Register Volume 77, Number 94 (Tuesday, May 15, 2012)]
[Proposed Rules]
[Pages 28541-28543]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2012-11755]
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DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
37 CFR Part 1
[Docket No.: PTO-P-2012-2018]
Request for Comments on the Recommendation for the Disclosure of
Sequence Listings Using XML (Proposed ST.26)
AGENCY: United States Patent and Trademark Office, Commerce.
ACTION: Request for comments.
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SUMMARY: The United States Patent and Trademark Office (Office) is
seeking comments to obtain views of the public on the international
effort to revise the standard for the presentation of nucleotide and/or
amino acid sequences and the consequent changes to the United States
rules of practice. The standard is being revised to require the use of
extensible mark-up language (XML) format, to update the standard, and
to more closely align requirements of the standard with those of public
sequence database providers. Comments may be offered on any aspect of
this effort.
DATES: Written comments must be received on or before July 16, 2012 to
ensure consideration. No public hearing will be held.
ADDRESSES: Comments concerning this notice should be sent by electronic
mail message over the Internet addressed to [email protected]. Comments may also be submitted by mail addressed to:
Mail Stop Comments-Patents, Commissioner for Patents, P.O. Box 1450,
Alexandria, VA 22313-1450, marked to the attention of Susan C. Wolski,
Office of Patent Cooperation Treaty Legal Administration, Office of the
Associate Commissioner for Patent Examination Policy. Although comments
may be submitted by mail, the Office prefers to receive comments via
the Internet.
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 via the
Internet (http://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: Susan C. Wolski, Office of Patent
Cooperation Treaty Legal Administration, Office of the Deputy
Commissioner for Patent Examination Policy, by telephone at (571) 272-
3304, or by mail addressed to: Mail Stop Comments--Patents,
Commissioner for Patents, P.O. Box 1450, Alexandria, VA 22313-1450,
marked to the attention of Susan C. Wolski.
SUPPLEMENTARY INFORMATION:
1. Background Information
Patent applicants are currently required to submit biological
sequence data in a standardized electronic format in accordance with
World Intellectual Property Organization (WIPO) Standard ST.25, both
within the framework of the Patent Cooperation Treaty (PCT) (Annex C of
the Administrative Instructions) and under most national and regional
provisions. The Rules of Patent Practice in the United States (37 CFR
1.821-1.825) are substantively consistent with WIPO ST.25.
WIPO ST.25, which became effective in 1998 and has not been revised
since that time, requires a flat file structure of numeric identifiers
using a limited set of character codes. In October 2010, the Committee
on WIPO Standards (CWS) established a Task Force, designating the
European Patent Organization (EPO) as the lead, to propose a revised
standard for the filing of nucleotide and/or amino acid sequence
listings in XML format (hereinafter referred to as ``the XML
standard''). The work of the Task Force is accomplished through online
collaboration, restricted to Task Force members only, via the WIPO Web
site. The XML standard (tentatively designated WIPO ST.26) is composed
of three documents, namely, the main body of the standard, a first
annex setting forth the controlled vocabularies for use with the
sequence part of the standard, and a second annex setting forth the
Document Type Definition (DTD) for the standard. Five rounds of
comment/revision have taken place since March 2011, and discussion of
the documents is ongoing.
It is expected that the XML standard will be adopted at a meeting
of the CWS in early 2013. However, no decision has been made as to when
it will enter into force for PCT purposes, and consequently, for
national and regional offices. The work of the Task Force and issues
pertaining to transitioning to the XML standard were discussed at the
Nineteenth Session of the Meeting of International Authorities
(MIA)(February 8-10, 2012). The Meeting agreed that the Task Force will
look at the feasibility of developing a tool that would allow for the
easy and complete conversion of sequence listings filed in one format
(ST.25 or XML) into the other. Thereafter, the appropriate PCT bodies
should commence a discussion on the most appropriate mechanism for
transition from ST.25 to the XML standard. See the Meeting Summary
available at http://www.wipo.int/edocs/mdocs/pct//en/pct_mia_19/pct_mia_19_13.pdf.
2. Request for Comments
The Office, leading the negotiations for the United States, is
seeking public comment on the current version of the main body of the
standard and its two annexes. The text of the current draft of the
proposed main body of the sequence listing standard, with its
associated Annexes, is available via the Office's Web site at http://www.uspto.gov/patents/law/comments/sequence_listings.jsp. The
documents are: Recommmendation for the disclosure of sequence listings
using XML (Proposed ST.26); Annex B.1. Controlled vocabularies; and
ST26SequenceListing-v1-0.
In light of the likely adoption of this standard in early 2013, the
Office desires to ensure that the XML standard is disseminated as
widely as possible and the opportunity to provide comments is
correspondingly comprehensive. Written comments may be offered on any
aspect of the proposed standard or Annexes, transition issues, or
expected implementation in the United States. Comments are specifically
requested on the following issues:
[[Page 28542]]
(1) Comprehensiveness and Clarity. One goal of the development of a
WIPO Standard for sequence listings is to allow patent applicants to
draw up a single sequence listing in a patent application that would be
acceptable for the purposes of both international and national or
regional prosecution. Any new standard should represent the maximum
requirements for any sequence listing submission, and each national and
regional office requiring compliance with the XML standard should have
consistent interpretations of the standard.
The Office invites comments on whether the main body of the
standard is sufficiently comprehensive and clear to achieve this goal,
and in particular welcomes suggestions to add details or clarify the
language as appropriate.
(2) Absence of PCT Procedure. Currently, ST.25 includes both
substantive and procedural requirements for sequence listings because
it fully incorporates PCT Adminstrative Instructions Annex C. The XML
standard will be limited to substantive requirements, consisting of a
general information part (to include information sufficient to identify
the application of which it is a part) and a sequence data part (to
include technical information pertaining to each sequence in the
listing). It is expected that the PCT Administrative Instructions will
be revised to separately specify procedural requirements pertaining to
sequence listings filed under the XML standard in international
applications. As an example, the XML standard itself will not require
translation of free text that is in a non-English language to be
included within the text of the application disclosure. However,
international, national and regional offices would be free to make such
a requirement.
The Office invites comments as to whether the XML standard includes
any unnecessary procedural requirements or excludes any procedural
requirements that should be retained.
(3) Feature Keys and Qualifiers. ST.25 uses a controlled vocabulary
of feature keys to describe nucleic acid and amino acid sequences, with
a very limited set of controlled vocabulary to further describe certain
features. The XML standard includes, in addition to feature keys, a
significant number of the qualifiers for the description of nucleotide
sequences agreed upon by the International Nucleotide Sequence Database
Collaboration (INSDC). Note that the XML standard does not include
feature keys and qualifiers that are not relevant for patent data
purposes. The XML standard also includes four qualifiers for amino
acids. These feature keys and qualifiers form part of Annex B.1.
The INSDC revises feature keys and qualifiers on an occasional
basis (i.e., there is no set schedule). While the goal of requiring
INSDC feature keys and qualifiers is to improve compatibility with the
public sequence database providers, it is not clear how often the
international, national, and regional offices will be able to update
submission software and procedures or rules to accommodate such
changes.
Public comment is invited with regard to any feature keys or
qualifiers that are not clear, or that are optional and should be
mandatory (or vice versa). Comments are also welcome regarding how
frequently WIPO should consider updating these feature keys and
qualifiers, recognizing the impact this will have on the Office rules.
(4) Definition of a Sequence for which a Sequence Listing is
Required. The XML standard revises the definition of a sequence for
which a sequence listing is required. The following list sets forth the
more significant differences from ST.25.
(a) Prohibited sequences. ST.25 describes sequences for which a
sequence listing is not required, but does not specifically prohibit
the presentation of such sequences. In contrast, the XML standard
(paragraph 4) prohibits the inclusion of any branched nucleotide or
amino acid sequences or any sequences with fewer than ten specifically
defined nucleotides or fewer than four specifically defined amino
acids.
(b) Modified nucleotides. ST.25 specifies that sequences comprising
nucleotides other than those listed in Appendix 2, Tables 1 and 2, are
specifically excluded from the definition of sequences for which a
sequence listing must be provided. In contrast, the XML standard
(paragraph 5) does not contain this exclusion, and specifies inclusion
of sequences containing any nucleotides that can be represented using
any of the symbols set forth in Annex B.1, paragraph 1, Table 1. This
includes nucleotides that may contain, inter alia, a modified or
synthetic purine or pyrimidine base; a modified or synthetic ribose or
deoxyribose, or a modified or synthetic 3' to 5' internucleotide
linkage, i.e., any chemical moiety that provides the same structural
function as the phosphate moiety of DNA or RNA.
(c) D-amino acids. ST.25 specifies that sequences containing at
least one D-amino acid are specifically excluded from the definition of
sequences for which a sequence listing must be provided. In contrast,
pursuant to the XML standard (paragraph 6), any unbranched sequences
containing four or more specifically defined amino acids would be
required to be included in a sequence listing, regardless of whether
that sequence contains any D-amino acids.
(d) Variants. ST.25 does not specifically address how variants are
to be represented in a sequence listing. The XML standard specifies how
variants are to be represented. See paragraph 58 which reads as follow:
58. A variant sequence disclosed by enumeration of its residues
and encompassed by paragraph 4 must be assigned its own sequence
identification number and be presented in the sequence listing. A
specific variant, i.e., deletion, addition, or substitution,
disclosed only by reference to a disclosed primary sequence in the
sequence listing, must be presented in the sequence listing either
as a separate sequence assigned its own sequence identification
number or by annotation of the primary sequence with appropriate
feature keys and qualifiers. A specific variant containing multiple
variations from the primary sequence at distinct locations, where
the variations at each location only occur together, must be
presented in the sequence listing as a separate sequence assigned
its own sequence identification number.
The Office requests comments on whether these changes as set forth
in paragraphs (a) through (d) above are desirable, and what
difficulties, if any, are likely to be faced in complying with the
definition in the XML standard.
(5) Publications (references). ST.25 provided for the inclusion of
publication information (i.e., references to relevant prior
publications) in numeric identifiers <300>-312>. The XML standard does
not provide for such references.
The Office invites comments as to whether there is any perceived
detriment due to the non-inclusion of such publications or references
in the sequence listing.
(6) Transition Issues. Transition to the XML standard will require
Office analysis of the time frame required to update systems to
receive, process, and search sequence listings filed under the
standard. The date of entry into force may be as long as two or three
years after adoption of the new standard; however, as noted above,
discussions within the Task Force and WIPO are continuing. Current
thinking in the Office is that it would be preferable to have a clean
transition from current WIPO Standard ST.25 to the XML Standard. This
would be accomplished by having the XML Standard enter into force for
PCT purposes (and correspondingly, for US applications at
[[Page 28543]]
the same time) at a particular date in the future (e.g., after such
date, all sequence listings filed for the first time in an application
(including a continuation, continuation-in-part, and a divisional)
would have to be filed in compliance with that new standard).
(a) The Office invites comments regarding how much time is likely
to be needed for applicants to transition to the XML standard (with the
assumption that sequence listing authoring software will be publicly
available).
(b) Given the divergent requirements of the proposed XML standard
and ST.25 as described above, the Office invites comments on what
difficulties an applicant should anticipate if national or regional
offices required compliance with different standards (i.e., ST.25 and
XML). Will the existence of separate authoring tools for each of the
standards mitigate such difficulties?
Dated: May 9, 2012.
David J. Kappos,
Under Secretary of Commerce for Intellectual Property and Director of
the United States Patent and Trademark Office.
[FR Doc. 2012-11755 Filed 5-14-12; 8:45 am]
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