81 FR 74775 - 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)

DEPARTMENT OF COMMERCE
Patent and Trademark Office

Federal Register Volume 81, Issue 208 (October 27, 2016)

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.

[Federal Register Volume 81, Number 208 (Thursday, October 27, 2016)]
[Notices]
[Pages 74775-74777]
From the Federal Register Online  [www.thefederalregister.org]
[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

[[Page 74776]]

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