[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]



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.


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.


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 
    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 
    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 
    (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 
    (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]