[Federal Register Volume 81, Number 208 (Thursday, October 27, 2016)]
[Notices]
[Pages 74775-74777]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2016-25968]
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DEPARTMENT OF COMMERCE
Patent and Trademark Office
[Docket No.: PTO-P-2016-0039]
Standard ST.26--Request for Comments on the Recommended Standard
for the Presentation of Nucleotide and Amino Acid Sequence Listings
Using XML (eXtensible Markup Language)
AGENCY: United States Patent and Trademark Office, Commerce.
ACTION: Request for comments.
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SUMMARY: Patent applications that contain disclosures of nucleotide
and/or amino acid sequences must contain sequence information in a
separate part of the disclosure in a specified manner. The United
States Patent and Trademark Office (Office) is seeking additional
comments to obtain views of the public on the continuing international
effort to revise the World Intellectual Property Organization (WIPO)
standard for the presentation of nucleotide and/or amino acid sequences
and the consequent changes to the United States rules of practice. The
revised standard will be known as WIPO Standard ST.26. An interim
version of WIPO Standard ST.26 was adopted in March 2016 by the
Committee on WIPO Standards (CWS), but has not been implemented pending
further consideration by the CWS. Since the adoption of the interim
version, efforts have been undertaken to finalize WIPO Standard ST.26
and to improve its effectiveness once implemented. One aspect of that
continuing effort is a proposed guidance document annex, which will
include a variety of sequence disclosure examples, to ensure
understanding and uniform application of standard requirements.
Comments may be offered on any aspect of this effort, and in
particular, (a) the comprehensiveness and clarity of WIPO Standard
ST.26 and the proposed guidance document annex, and (b) the proposed
authoring/validation tool for creation of a sequence listing in XML.
DATES: Written comments must be received on or before December 27, 2016
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
International Patent Legal Administration, Office of the Deputy
Commissioner for International Patent Cooperation. 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
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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
International Patent Legal Administration, Office of the Deputy
Commissioner for International Patent Cooperation, 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
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) were amended to
implement WIPO Standard ST.25 in July of 1998. See Requirements for
Patent Applications Containing Nucleotide Sequences and/or Amno Acid
Disclosures, 63 FR 29620 (June 1, 1998), 1121 Off. Gaz. Pat. Office 82
(June 23, 1998).
WIPO Standard 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 CWS established a Task Force, designating the European Patent
Organization as the lead, to draft a revised standard (WIPO Standard
ST.26) for the filing of nucleotide and/or amino acid sequence listings
in XML format. The Office issued a first request for comments on WIPO
Standard ST.26 as drafted by the Task Force (see Request for Comments
on the Recommendation for the Disclosure of Sequence Listings Using XML
(Proposed ST.26), 77 FR 28541 (May 15, 2012), 1379 Off. Gaz. Pat.
Office 106 (June 12, 2012)), following which the draft was revised in
response to comments received. In March 2016, the reconvened fourth
session of the CWS adopted an interim version of WIPO Standard ST.26,
which had been initially considered at the fourth session of the CWS in
May 2014. The interim version of WIPO Standard ST.26 contains an
editorial note requesting that implementation be postponed until the
recommendation for the transition from WIPO Standard ST.25 to WIPO
Standard ST.26 is agreed on by the CWS at its next session to be held
in 2017. Meanwhile, WIPO Standard ST.25 should continue to be used. The
adopted interim version of WIPO Standard ST.26 is composed of six
documents, namely, the main body of the standard, a first annex setting
forth the controlled vocabulary for use with the sequence part of the
standard, a second annex setting forth the Document Type Definition
(DTD) for the standard, a third annex containing a sequence listing
specimen, a fourth annex setting forth the character subset from the
Unicode Basic Latin Code Table, and a fifth annex setting forth
additional data exchange requirements for patent offices, and can be
found here: http://www.wipo.int/export/sites/www/standards/en/pdf/03-26-01.pdf. Since the adoption of the interim version, the main body,
the controlled vocabulary, and the DTD have been further revised and
updated. In addition, a sixth annex has been proposed; it would contain
a guidance document that aims to ensure that all applicants and
Intellectual Property Offices (IPOs) understand and agree on the
requirements for inclusion and representation of sequence disclosures.
In all, seven rounds of discussion have been completed since March
2011, and currently, the eighth round of discussion of the documents is
ongoing.
2. Request for Comments
The Office, leading the negotiations for the United States, is
seeking public comment on WIPO Standard ST.26, as revised subsequent to
the adoption of the interim version. To that end, the current revisions
of the main body of the standard and its five annexes, as well as the
newly proposed sixth annex, are available via the Office's Web site at
http://www.uspto.gov/patent/laws-and-regulations/comments-public/2016-comments-standard-st26-presentation-nucleotide-and.
Written comments may be offered on any aspect of WIPO Standard
ST.26, its annexes, or the proposed authoring/validation tool. Comments
are specifically requested on the following issues:
(a) WIPO Standard ST.26 Main Body
Since the first request for comments, the main body of WIPO
Standard ST.26 has been revised, inter alia, to define a ``nucleotide''
to include nucleotide analogues and to provide further guidance on
representation of nucleotide analogue sequences and variant sequences
that have been disclosed as a single sequence with enumerated
alternative variant residues at one or more positions.
The Office invites comments on whether the main body of WIPO
Standard ST.26 is sufficiently comprehensive and clear, and in
particular welcomes suggestions to add details or clarify the language
as appropriate.
(b) Guidance Document
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
worldwide. Any new standard should represent the maximum requirements
for any sequence listing submission. The purpose of the guidance
document is to ensure that all applicants and IPOs understand and agree
on the requirements for inclusion and representation of sequence
disclosures, such that this purpose is realized.
The guidance document is composed of an introduction, examples, and
a sequence listing in XML demonstrating representation of the
exemplified sequences. The introduction defines terminology used in the
document and discusses the questions raised for each example, namely,
whether inclusion is required for a particular disclosed sequence, if
inclusion of the sequence is permitted when it is not required, and the
appropriate means of representation of sequences included in a sequence
listing. Examples were chosen to illustrate various paragraphs of the
main body and include 22 involving nucleotide sequences and 19
involving amino acid sequences. It is envisioned that the guidance
document would be updated as necessary to include further examples to
keep pace with technological advances.
The Office invites comments on whether the guidance document is
sufficiently comprehensive and clear, and in particular welcomes
suggestions to add details or further examples as appropriate.
(c) Authoring and Validation Tool
Availability of an authoring tool in advance of the WIPO Standard
ST.26 effective date is key to a successful transition from WIPO
Standard ST.25. As envisioned, the authoring tool should be capable of
intake of a sequence listing in WIPO Standard ST.25 format, and with
additional input from applicant, create a sequence listing in WIPO
Standard ST.26 format. Unfortunately, direct conversion from one
standard to the other is not possible, due to numerous differences
between the two standards, including inter alia,
[[Page 74777]]
the types of required sequences, representation and annotation of the
sequences, and sequence data structure.
The authoring tool should also prompt entry of all required data,
prevent entry of sequences having fewer than ten specifically defined
nucleotides or fewer than four specifically defined amino acids, inform
as to the possibility of optional annotations, and allow use of only
acceptable values or formats where applicable, thereby enhancing
submission quality. A sequence listing in WIPO Standard ST.26 XML
format is not as easily human-readable as its ST.25 counterpart;
therefore, the tool should also provide a means for easily viewing both
the in-progress and completed sequence listing.
Because the authoring tool is expected to prompt entry of all
required data and to allow use of only acceptable values or formats
where applicable, a certain level of validation occurs as data is
entered. The tool is further expected to include a separate validation
function for use by both applicants and IPOs.
WIPO Standard ST.25 provides for a single numeric identifier <223>
per sequence to contain ``free text'' to describe sequence
characteristics using non-language neutral vocabulary. Such ``free
text'' is required to be repeated in the main part of the application
description in the language thereof in a specific recommended section
entitled ``Sequence Listing Free Text.'' Such repetition ensures that
any ``free text'' will be translated together with the application
description, precluding the need for separate translation of the
sequence listing itself. In contrast, WIPO Standard ST.26 allows use of
``free text'' as the value for multiple different annotation qualifiers
per sequence, and due to the absence of procedural requirements,
repetition in the application is not required, although such a
requirement under the PCT and by various IPOs is possible. In WIPO
Standard ST.26, ``free text'' is limited to a few short terms
indispensable for understanding a characteristic of a sequence, is
preferably in the English language, and as part of the sequence data
part of the sequence listing, must not exceed 1000 characters composed
of printable characters from the Unicode Basic Latin code table. It is
expected that most inventors providing sequence information are capable
of providing ``free text'' in the English language.
The Office invites comments on any aspect of the authoring tool,
and in particular welcomes feedback on whether it is deemed necessary
for the authoring tool to include a mechanism for automatic
identification and extraction of any ``free text'' from sequence
annotations to facilitate inclusion in the application description.
Dated: October 21, 2016.
Michelle K. Lee,
Under Secretary of Commerce for Intellectual Property and Director of
the United States Patent and Trademark Office.
[FR Doc. 2016-25968 Filed 10-26-16; 8:45 am]
BILLING CODE 3510-16-P