[Federal Register Volume 87, Number 98 (Friday, May 20, 2022)]
[Rules and Regulations]
[Pages 30806-30821]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2022-10343]
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DEPARTMENT OF COMMERCE
Patent and Trademark Office
37 CFR Part 1
[Docket No. PTO-P-2021-0006]
RIN 0651-AD53
Standard for Presentation of Nucleotide and Amino Acid Sequence
Listings Using eXtensible Markup Language (XML) in Patent Applications
To Implement WIPO Standard ST.26; Incorporation by Reference
AGENCY: United States Patent and Trademark Office, Department of
Commerce.
ACTION: Final rule.
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SUMMARY: The United States Patent and Trademark Office (USPTO or
Office) is amending the rules of practice for submitting biological
sequence data associated with disclosures of nucleotide and amino acid
sequences in patent applications by incorporating by reference certain
provisions of World Intellectual Property Office Standard ST.26 (WIPO
Standard ST.26) into the USPTO rules of practice. Other conforming
changes to accommodate the new rules of practice based on the new
standard are also included. In addition to simplifying the process for
applicants filing in multiple countries, the requirement to submit a
single sequence listing in eXtensible Markup Language (XML) format, or
``Sequence Listing XML,'' will result in better preservation,
accessibility, and sorting of the submitted sequence data for the
public.
DATES: Effective date: This final rule is effective on July 1, 2022.
The incorporation by reference of certain publications listed in this
rule is approved by the Director of the Federal Register as of July 1,
2022.
Applicability date: Patent applications filed on or after July 1,
2022, having disclosures of nucleotide and/or amino acid sequences as
defined in 37 CFR 1.831(b) must comply with new rules for submission of
a ``Sequence Listing XML'' in accordance with 37 CFR 1.831 through
1.835. All other provisions of this final rule apply to all patent
applications filed before, on, or after July 1, 2022.
FOR FURTHER INFORMATION CONTACT: Mary C. Till, Senior Legal Advisor,
Office of Patent Legal Administration, Office of the Deputy
Commissioner for Patents, at [email protected] or 571-272-7755; or
Ali Salimi, Senior Legal Advisor, Office of Patent Legal
Administration, Office of the Deputy
[[Page 30807]]
Commissioner for Patents, at [email protected] or 571-272-0909.
SUPPLEMENTARY INFORMATION:
Table of Contents
I. Background
a. Summary of Changes
b. Introduction
c. Incorporation by Reference of WIPO Standard ST.26
d. Benefits
e. WIPO Authoring and Validation Tool (WIPO Sequence)
f. Applicability
II. Discussion of Specific Rules
III. Comments and Responses
IV. Rulemaking Considerations
I. Background
a. Summary of Changes
WIPO Standard ST.26 is the new international standard developed and
adopted by WIPO and member states for purposes of presenting
biotechnology information in patent applications. It will apply to
international and national applications filed on or after July 1, 2022.
New provisions in 37 CFR 1.831 through 1.835 implement WIPO Standard
ST.26. Applications pending prior to July 1, 2022, will not have to
comply with WIPO Standard ST.26; rather, such applications will require
the submission of a ``Sequence Listing,'' as defined in 37 CFR
1.821(a), in compliance with 37 CFR 1.8211.825.
Under WIPO Standard ST.26 (as implemented by 37 CFR 1.831 through
1.835), patent applications that contain disclosures of nucleotide and/
or amino acid sequences must present the associated biological sequence
data in a standardized electronic format (a ``Sequence Listing XML'')
as a separate part of the specification. In particular, WIPO Standard
ST.26 permits applicants to submit a single, internationally acceptable
sequence listing in a language-neutral format using specified
International Nucleotide Sequence Database Collaboration (INSDC)
identifiers in international applications filed under the Patent
Cooperation Treaty (PCT) and in national and regional applications in
the intellectual property offices (IPOs) of WIPO member states. As a
result, a single sequence listing in compliance with WIPO Standard
ST.26 can be prepared for use in the IPOs of WIPO member states.
For applications filed on or after July 1, 2022, the changes in
this final rule include the: (1) Creation of new rules (37 CFR 1.831
through 1.839) that incorporate by reference WIPO Standard ST.26; (2)
use of INSDC sequence data elements to replace numeric identifiers used
in the previous Standard ST.25 for the submission of nucleotide and/or
amino acid sequences; (3) modification of rules of practice to include
reference to a ``Sequence Listing XML''; (4) elimination of the ability
to file a paper or Portable Document Format (PDF) copy of nucleotide
and/or amino acid sequences; (5) elimination of the option to include
within a ``Sequence Listing XML,'' sequences with fewer than 4
specifically defined amino acids and fewer than 10 specifically defined
nucleotides; and (6) clarification and simplification of the rules to
aid in understanding the requirements set forth.
b. Introduction
In an effort to streamline and reduce existing procedural
requirements and to implement WIPO Standard ST.26, the USPTO is
amending its rules of practice (by adding 37 CFR 1.831 through 1.839)
for submitting biological sequence data associated with disclosures of
nucleotide and/or amino acid sequences in patent applications filed on
or after July 1, 2022. These changes also respond to the needs of our
customers to comply with WIPO Standard ST.26.
To decrease the burden on applicants who file patent applications
containing nucleotide and/or amino acid sequences internationally, the
USPTO has worked with other WIPO member states as part of the Committee
on WIPO Standards (CWS) to develop a single, internationally acceptable
sequence listing standard for use in patent applications filed in those
member states. Beginning in October of 2010, the CWS established a task
force to propose a revised standard for the filing of nucleotide and/or
amino acid sequence listings in XML file format. To obtain public input
on the content of WIPO Standard ST.26, the USPTO issued requests for
comments in 2012 and 2016. See Request for Comments on the
Recommendation for the Disclosure of Sequence Listings Using XML
(Proposed ST.26), 77 FR 28541 (May 15, 2012); and 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), 81 FR 74775 (October 27, 2016). The adopted version
of WIPO Standard ST.26 takes those comments into account. To achieve
the goals WIPO and its member states (including the United States) set
out by developing the sequence listing standard for presenting data
consistently across all IPOs, all WIPO member states agreed to
implement WIPO Standard ST.26 for international and national
applications filed on or after July 1, 2022. Therefore, in view of this
final rule, applications filed in the United States on or after July 1,
2022, will need to conform to WIPO Standard ST.26 as implemented in 37
CFR 1.831 through 1.839, which requires submitting sequence listings in
XML format.
Under the final rule, applications that claim benefit or priority
to an earlier application, where the earlier application contained a
sequence listing that complied with the requirements of Standard ST.25
or other earlier requirements, must comply with the new rules that
incorporate by reference WIPO Standard ST.26. To facilitate compliance,
WIPO, with input from WIPO member states, developed WIPO Sequence, a
sequence listing authoring and validating tool that applicants can use
to prepare and validate their sequence listings in XML format, as
discussed below. The USPTO is adding to the patent rules (37 CFR part
1) by incorporating by reference WIPO Standard ST.26, and providing
conforming amendments to the current rules.
To ensure that biological sequence data associated with the
disclosures of nucleotide and/or amino acid sequences in patent
applications can be widely disseminated and searchable by the public
and IPOs, the USPTO works with the National Center for Biotechnology
Information (NCBI) on the inclusion of patent sequence data in the
GenBank searchable database. For the NCBI to include all sequence data
from the USPTO, the data must be provided in INSDC format so it is
compatible with GenBank. The Standard ST.25 format sequence listings
cannot be readily converted to INSDC format, resulting in only a
fraction of patent sequence information appearing in GenBank. This data
loss limits the sequence information available to the public and
exchanged with other sequence database providers (e.g., the National
Institute of Genetics (NIG) in Japan, the DNA Data Bank of Japan
(DDBJ), and the European Molecular Biology Laboratory, European
Bioinformatics Institute (EMBL-EBI). WIPO has been working with the
WIPO member states to create, adopt, and implement WIPO Standard ST.26
for sequence listing submissions in XML file format, which has the
INSDC data elements to address the data loss. WIPO Standard ST.26 aims
to enhance the accuracy and quality of biological sequence data that is
publicly disseminated. With the adoption and implementation of WIPO
Standard ST.26, more complete biological sequence data from patents and
patent applications will be included in GenBank and thus be accessible
by the
[[Page 30808]]
public. The change from American Standard Code for Information
Interchange (ASCII) plain text format to XML format will result in
sequence data having computer tags that facilitate sorting and
retrieving and will permit ease of access to the data. Additionally,
the NCBI plans to stop accepting data in Standard ST.25 format for
inclusion in GenBank approximately three to five years after the WIPO
Standard ST.26 transition date (July 1, 2022).
c. Incorporation by Reference of WIPO Standard ST.26
The WIPO ``Handbook on Industrial Property Information and
Documentation'' sets forth standards for the presentation of data in
many contexts. WIPO Standard ST.26 is titled ``RECOMMENDED STANDARD FOR
THE PRESENTATION OF NUCLEOTIDE AND AMINO ACID SEQUENCE LISTINGS USING
XML (EXTENSIBLE MARKUP LANGUAGE).'' The CWS adopted the current version
(version 1.5) in November of 2021. In October of 2021, at the
Assemblies of Member States of WIPO, the member states agreed on July
1, 2022, as the implementation date of WIPO Standard ST.26. This final
rule incorporates by reference WIPO Standard ST.26. The standard is
available from WIPO, 34 chemin des Colombettes, 1211 Geneva 20
Switzerland, www.wipo.int. and also as provided for in 37 CFR 1.839.
WIPO Standard ST.26 is composed of eight documents, namely, the
main body of the standard, a first annex (Annex I) setting forth the
controlled vocabulary for use with the main body, a second annex (Annex
II) setting forth the Document Type Definition (DTD) for the Sequence
Listing, a third annex (Annex III) containing a sequence listing
specimen (XML file), a fourth annex (Annex IV) setting forth the
character subset from the Unicode Basic Latin Code Table, a fifth annex
(Annex V) setting forth additional data exchange requirements for IPOs,
a sixth annex (Annex VI) containing a guidance document with
illustrated examples, and a seventh annex (Annex VII) setting forth
recommendations for the transformation of a sequence listing from
Standard ST.25 format to WIPO Standard ST.26 format, including guidance
on how to avoid adding or deleting subject matter.
The main body of WIPO Standard ST.26 defines the disclosures of
nucleotide and/or amino acid sequences in patent applications that must
be presented in a sequence listing in XML format in the manner
specified in the standard. As detailed in paragraph eight of the main
body, a sequence listing in XML format must not include any sequences
having fewer than 10 specifically defined nucleotides, or fewer than 4
specifically defined amino acids. If such sequences are included in the
disclosure, they must not be assigned a sequence identification number.
The main body establishes the requirements for the representation of
nucleotide and/or amino acid sequences and the requirements for the XML
file format for a sequence listing. Annex I contains controlled
vocabulary that provides nucleotide base codes, lists of modified
nucleotides and their abbreviations, amino acid codes, and a list of
modified amino acids and their abbreviations. In addition, Annex I
provides defined feature keys and qualifiers used for nucleotide and/or
amino acid sequences in the XML file for a sequence listing. Annex I
specifically identifies qualifiers with language-dependent ``free
text'' values that may require translation for national and regional
procedures. Annex II provides the DTD setting forth the technical
specifications to which a submitted Sequence Listing XML must conform.
Annex III provides a link to a specimen of a sequence listing that is
compliant with WIPO Standard ST.26 and that shows a representation of
an entire sequence listing in XML format. Annex IV provides a table of
the character subset from the Unicode Basic Latin Code that will be
used in the XML file for the sequence listing. Annex V provides
guidance to WIPO member states on how certain sequence elements should
be populated when data is exchanged with database providers. Annex VI,
containing the guidance document, ensures that all applicants and WIPO
member states understand the requirements for inclusion and
representation of sequence disclosures. This guidance document was
developed, in part, to address concerns raised in response to the
USPTO's requests for comments in 2012 and 2016, mentioned above. The
guidance document illustrates the requirements of selected paragraphs
in the main body of WIPO Standard ST.26 through specific examples of
nucleotide and amino acid biological sequence data. Additionally, the
document provides guidance on the manner in which biological sequence
data is represented in a sequence listing in XML format that is
compliant with WIPO Standard ST.26. Annex VII addresses the mandatory
requirements of WIPO Standard ST.26, and the potential consequence of
these requirements when transforming a compliant Standard ST.25
sequence listing into a WIPO Standard ST.26 sequence listing. Annex VII
also provides detailed guidance on how to avoid adding or deleting
subject matter due to the additional requirements of WIPO Standard
ST.26.
d. Benefits
Transitioning from rules based on WIPO Standard ST.25 (i.e., the
basis for USPTO rules 37 CFR 1.821 through 1.825, regarding ``Sequence
Listings'') to rules based on WIPO Standard ST.26 will be beneficial to
both patent applicants filing sequence listings and IPOs receiving
applications containing disclosures of nucleotide and/or amino acid
sequences requiring sequence listings. WIPO Standard ST.26 provides
clear requirements for what must be included in a sequence listing and
how sequences must be represented. For example, it standardizes the
representation of modified nucleotide sequences and amino acid
sequences as well as variants derived from primary sequences. Since
WIPO Standard ST.26 contains a guidance document that illustrates the
requirements for the inclusion and representation of biological
sequence data, patent applicants will have a better understanding of
the requirements for the presentation of biological sequence data in a
compliant sequence listing under WIPO Standard ST.26 (as implemented by
37 CFR 1.831 through 1.839). Additionally, since WIPO Standard ST.26
only allows XML format (an electronic computer readable format), this
final rule eliminates the potential for differences between a sequence
listing filed in paper/PDF format and the required electronic computer
readable format (CRF). As a further benefit, the IPOs of WIPO member
states will no longer need to expend resources to process paper
sequence listings and perform necessary checks on the contents of paper
documents.
Unlike rules based on Standard ST.25, rules based on WIPO Standard
ST.26 will allow patent applicants to file a single sequence listing
with the USPTO (with the exception of changes to comply with national
language requirements) that will be acceptable to the IPOs of all WIPO
member states. Under Standard ST.25, IPOs have interpreted and enforced
rules differently due to the imprecise language in that standard. This
has resulted in the frustrating situation in which applicants generate
sequence listings that may be accepted in one IPO but not another.
WIPO Standard ST.26 was drafted to precisely define what must and
must not be included in a sequence listing
[[Page 30809]]
and how sequences must be represented in a sequence listing. The
``Guidance document with illustrated examples'' in Annex VI of WIPO
Standard ST.26 demonstrates the application of the rules to real-world
sequence disclosure examples, reducing the possibility of
misinterpretation by IPOs or applicants.
Due to the improved data structure of XML, transitioning to rules
based on WIPO Standard ST.26 will increase the quality of the
examination of patent applications containing biological sequence data
since a more comprehensive search will be possible. Sequence listings
submitted in accordance with WIPO Standard ST.26 allow for targeted
searching of both sequence annotation and newly required sequence
types, such as D-amino acids, nucleotide analogues, and linear portions
of branched sequences. Finally, sequence listing submissions under
rules based on WIPO Standard ST.26 will enhance public database
content, as they include the sequence annotations (e.g., feature keys
and qualifiers) used by database providers to describe biological
sequence data. WIPO Standard ST.26 standardizes sequence variant
presentation, the annotation of modified and unusual residues, feature
location descriptors, the use of feature keys and qualifiers, organism
names, and the presentation of coding regions. Incorporation by
reference of WIPO Standard ST.26 into USPTO rules promotes data
exchange between the USPTO and the NCBI due to the use of INSDC
identifiers required by database providers. The presence of additional
data, as well as the enhanced compatibility to facilitate the exchange
of data, will increase the value of database searches that relate to
nucleotide and amino acid sequences for biotechnology stakeholders.
Requiring compliance with WIPO Standard ST.26 for an application
filed on or after July 1, 2022, will reduce the complexity and cost of
the long-term maintenance of information technology (IT) systems for
accepting sequence listings in multiple formats, provide a clear
implementation date, and facilitate the transition to the format
requirements of database providers. In addition, a requirement to
submit a single sequence listing in XML format will result in better
preservation, accessibility, and sorting of the submitted sequence data
for the public.
e. WIPO Authoring and Validation Tool (WIPO Sequence)
To comply with rules based on WIPO Standard ST.26, patent
applicants will be able to generate a sequence listing compliant with
WIPO Standard ST.26 using WIPO Sequence, a desktop application
developed by WIPO and adopted by WIPO member states. WIPO Sequence has
two functions: An authoring function and a validation function. Patent
applicants will be able to author and validate their sequence listing
using WIPO Sequence to comply with the requirements of WIPO Standard
ST.26. Such a sequence listing will be accepted by all the IPOs of the
WIPO member states. Thus, the burden of generating a sequence listing
that is acceptable across all WIPO member states will be significantly
decreased for patent applicants under WIPO Standard ST.26. This tool is
downloadable, free of charge, from the WIPO website. The current
version of WIPO Sequence is accessible at www.wipo.int/standards/en/sequence/index.html. This version, subject to updates, will allow the
public to become familiar with the tool and its dual functionalities.
WIPO Sequence will allow a user to create and save (author) patent
application data and biological sequence data in a project, validate
the project to ensure all required information is present, and generate
a sequence listing in WIPO Standard ST.26 XML format. Information can
be entered into a project manually, or data can be imported from a
source file in one of a number of file types. WIPO Sequence can import
data from other WIPO Standard ST.26 projects, WIPO Standard ST.26 XML
sequence listings, Standard ST.25 sequence listing text files, raw
files, multi-sequence format files, and FASTA (FAST-All-a DNA and
protein sequence alignment software package) files. Feature keys,
qualifiers, and organism names are available to select from drop-down
lists, simplifying the creation of sequence listings. Applicant and
inventor names, as well as custom organism names, can be stored in WIPO
Sequence for easy access. To facilitate the review of data entered into
a project, WIPO Sequence can generate a ``human-readable'' version (a
text version of the sequence data) of the sequence listing in addition
to the XML sequence listing.
WIPO Sequence includes an integrated validation function that will
alert users to most errors in a project or sequence listing data. The
validation function generates a report that clearly lists every
detected error, the location of the error, and the detected value of
the error, along with a link to the sequence in question, thereby
ensuring users can correct errors before generating a final sequence
listing. While the validation function will alert a user to most errors
in a project or sequence listing, there are a small number of errors
that can be detected only by human review (for example, an
inappropriate organism name). In those cases, the integrated validation
function will list a ``warning'' in the validation report, reminding
users of the applicable/relevant rule and urging them to check their
input values before generating a final sequence listing.
A sequence listing in Standard ST.25 format cannot automatically be
converted into WIPO Standard ST.26 format because certain data elements
required for a sequence listing compliant with WIPO Standard ST.26 are
not present in Standard ST.25. Therefore, conversion of a sequence
listing in Standard ST.25 format to Standard ST.26 format necessarily
requires additional input from the applicant. WIPO Sequence,
supplemented by significant guidance from WIPO and the USPTO (in Annex
VI and Annex VII of WIPO Standard ST.26), will help applicants
accomplish this task. Users can import a Standard ST.25 sequence
listing into a project, and WIPO Sequence automatically performs many
of the necessary conversions. An Import Report is generated that alerts
the user to all data conversions and lists all sequence entries that
require additional input. In response to concerns raised regarding the
USPTO's requests for comments in 2012 and 2016, the USPTO, in
conjunction with WIPO, developed Annex VII to provide detailed guidance
to help applicants avoid added or deleted subject matter when
converting a sequence listing from Standard ST.25 format into Standard
ST.26 format.
To ensure that IPOs can validate and accept sequence listing
projects from applicants generated with WIPO Sequence, WIPO is
developing a Standard ST.26 sequence listing validation tool, WIPO
Sequence Validator. WIPO Sequence Validator will be for use by IPOs.
WIPO Sequence Validator will be synchronized with the validation
function in the WIPO Sequence tool. The USPTO is integrating WIPO
Sequence Validator into its internal IT systems. The WIPO Sequence
Validator will apply the same validation rules as WIPO Sequence.
Therefore, filers will have a greater level of confidence that a
sequence listing authored and validated by WIPO Sequence will comply
with the USPTO rules for a ``Sequence Listing XML'' (37 CFR 1.831
through 1.835) and be accepted, given that the WIPO Sequence Validator
that the USPTO will use is based on WIPO Standard ST.26.
[[Page 30810]]
f. Applicability
In accordance with this final rule, an application that has a
filing date on or after July 1, 2022, will be required to provide a
``Sequence Listing XML'' in accordance with 37 CFR 1.831 through 1.835
for disclosures of any nucleotide and/or amino acid sequences that meet
the definitions of 37 CFR 1.831(a) and (b). This includes applications
having an international filing date on or after July 1, 2022, that
claim benefit or priority to applications with filing dates before July
1, 2022. Such applications include, but are not limited to,
applications having one or more benefit or priority claims under 35
U.S.C. 119(e) (claiming the benefit of a provisional), 35 U.S.C. 120
(claiming the benefit as a continuation and/or continuation-in-part),
35 U.S.C. 121 (claiming the benefit as a divisional), 35 U.S.C. 365(c)
(claiming the benefit as a continuing application to a PCT
application), or 35 U.S.C. 119(a)-(d) or 35 U.S.C. 365(a) (claiming the
priority to a foreign filed application or a prior filed PCT). If a
prior application to which benefit or priority is claimed contains a
``Sequence Listing'' in Standard ST.25 format (in compliance with 37
CFR 1.821 through 1.825), the applicant will be required to convert
that ``Sequence Listing'' to WIPO Standard ST.26 format (a ``Sequence
Listing XML'' in compliance with 37 CFR 1.831 through 1.835) for
inclusion in the new application filed on or after July 1, 2022.
As provided in 35 U.S.C. 363, the filing date of an international
stage application is also the filing date for the national stage
application filed under 35 U.S.C. 371. Accordingly, for applications
submitted under 35 U.S.C. 371, WIPO Standard ST.26 will apply to such
applications based on the international filing date of the
corresponding international application, rather than the date of
submission of the national stage application in the USPTO.
Compliance with 37 CFR 1.831 through 1.835 (rules based on WIPO
Standard ST.26) is also applicable to any reissue application filed on
or after July 1, 2022, where the disclosure or claims contain
nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(a) or
(b). The filing date of the originally granted patent for which reissue
is sought is not relevant in determining the applicability date of this
final rule.
Relying on the actual filing date of an application to determine
whether sequence information must conform to 37 CFR 1.821 through 1.825
(rules based on Standard ST.25) or 37 CFR 1.831 through 1.835 (rules
based on WIPO Standard ST.26) will simplify the application of the
sequence rules, both for the USPTO and the applicant. Though 37 CFR
1.821 through 1.825 are not revised by this final rule, note that 37
CFR 1.821 through 1.825 will not be applicable to applications filed on
or after July 1, 2022, as a result of this final rule.
For applications filed on or after July 1, 2022, the USPTO patent
electronic filing system will prohibit an applicant from submitting
both a ``Sequence Listing XML'' (a sequence listing that conforms to
WIPO Standard ST.26 as implemented in 37 CFR 1.831 through 1.835) and a
``Sequence Listing'' (a sequence listing that conforms to ST.25 as
implemented in 37 CFR 1.821 through 1.825) in the same submission.
Filing a ``Sequence Listing'' in an application filed on or after July
1, 2022, will result in a notice informing applicant that the
submission fails to comply with 37 CFR 1.831 through 1.834 and will
require submission of a ``Sequence Listing XML.''
While implementing regulations and procedures for ST.26, the USPTO
recognized that an applicant might erroneously provide a ``Sequence
Listing'' (one in ASCII plain text file format) even though a
``Sequence Listing XML'' is required. Therefore, in the rare
circumstance in which a ``Sequence Listing'' is submitted in an
application filed on or after July 1, 2022, the ``Sequence Listing''
present in the Office file wrapper of the application at issue may be
used to provide support for the submission of a compliant ``Sequence
Listing XML.'' The applicant's reliance on the ``Sequence Listing'' to
support the compliant ``Sequence Listing XML'' would be by way of the
safeguard under 37 CFR 1.57(b), if an earlier filed application
contains a proper ``Sequence Listing'' in .txt file format, or via a
grantable petition under 37 CFR 1.182, only if the application does not
have a proper benefit or priority claim present on the filing date to
an earlier filed application.
An applicant may rely on the provisions in 37 CFR 1.57(b), as
described in the Manual of Patent Examining Procedure at section 217,
to support the required ``Sequence Listing XML'' as an ``inadvertently
omitted portion of the specification or drawing(s).'' To rely on 37 CFR
1.57(b), a compliant ``Sequence Listing'' must have been submitted in
an earlier filed application to which the present application makes a
proper benefit or priority claim, and the ``Sequence Listing'' was
present on the filing date of the earlier filed application (i.e., the
earlier filed application contains a compliant ``Sequence Listing''
submitted under 37 CFR 1.821(c)(1) as an ASCII plain text file (with a
proper incorporation by reference statement in the specification), 37
CFR 1.821(c)(2) as a PDF copy, or 37 CF 1.821(c)(3) on physical sheets
of paper). An applicant would be required to submit: (1) A compliant
``Sequence Listing XML'' under 37 CFR 1.835(a)(1); (2) a statement
identifying where the inadvertently omitted portion of the
specification can be found (e.g., identifying the nucleotide and/or
amino acid sequence information in the compliant ``Sequence Listing''
from the earlier filed application that forms the basis for the
``Sequence Listing XML''), see 37 CFR 1.835(a)(3); (3) a statement
identifying the nucleotide and/or amino acid sequences of the
``Sequence Listing,'' submitted (in the earlier filed application)
under 37 CFR 1.821(c)(1) as an ASCII plain text file (with a proper
incorporation by reference statement in the specification), 37 CFR
1.821(c)(2) as a PDF copy, or 37 CFR 1.821(c)(3) as physical sheets of
paper, which forms the basis for the compliant ``Sequence Listing
XML''; (4) a statement that the ``Sequence Listing XML'' does not
introduce new matter into the application, see 37 CFR 1.835(a)(4); and
(5) a statement that all or a portion of the specification or drawings,
as found in the ``Sequence Listing XML,'' were inadvertently omitted
from the application. The availability of relief under 37 CFR 1.57(b)
precludes the filing of a grantable petition under 37 CFR 1.182 seeking
the same relief.
A petition under 37 CFR 1.182 would require: (1) A compliant
``Sequence Listing XML'' under 37 CFR 1.835(a)(1); (2) a statement
identifying the nucleotide and/or amino acid sequence information of
the ``Sequence Listing'' submitted as an ASCII plain text file that
forms the basis for the ``Sequence Listing XML'' (i.e., identifying the
nucleotide and/or amino acid sequence information found in the
``Sequence Listing'' from the earlier submitted ASCII ``Sequence
Listing'') that is relied on for submission of a compliant ``Sequence
Listing XML,'' see 37 CFR 1.835(a)(3); and (3) a statement that the
``Sequence Listing XML'' does not introduce new matter into the
application, as required by 37 CFR 1.835(a)(4). In such circumstances,
for record retention purposes, any ``Sequence Listing'' submitted as an
ASCII plain text file will be retained in the official record for the
application.
[[Page 30811]]
II. Discussion of Specific Rules
Section 1.52: Section 1.52 (e)(1)(ii) is amended to include
reference to a ``Sequence Listing XML'' submitted under Sec. 1.831(a)
in compliance with Sec. Sec. 1.832 through 1.834.
Section 1.52(e)(3)(iii) is amended to more explicitly indicate that
the contents of each read-only optical disc must be in ASCII plain text
and if compressed, must be compressed in accordance with Sec. 1.58 for
``Large Tables,'' Sec. 1.96 for a ``Computer Program Listing
Appendix,'' or Sec. 1.824 for a ``Sequence Listing'' or CRF of the
``Sequence Listing,'' as applicable.
Section 1.52(e)(3)(iv) is added to require that the contents of
each read-only optical disc for a ``Sequence Listing XML'' must be in
XML file format and, if compressed, must be compressed in accordance
with Sec. 1.834.
Section 1.52(e)(7) is amended to add that any amendment to the
information on a read-only optical disc previously submitted in
relation to a ``Sequence Listing XML'' must be made by way of a
replacement read-only optical disc in accordance with Sec. 1.835(b).
Section 1.52(f)(1) is amended to add that any XML file submitted on
a read-only optical disc is excluded from the application size fee
determination if the read-only optical disc contains a ``Sequence
Listing XML'' in compliance with Sec. 1.831(a). The provision at 35
U.S.C. 41(a)(1)(G) provides the basis for excluding ``any sequence
listing,'' when filed in electronic medium, from the application size
fee determination. A ``Sequence Listing XML'' is considered as ``any
sequence listing.''
Section 1.52(f)(1)(i) is amended to reference any ``Sequence
Listing XML'' in compliance with Sec. 1.831(a).
Section 1.52(f)(2) is amended to indicate that any XML file,
submitted via the USPTO patent electronic filing system for a
``Sequence Listing XML'' in compliance with Sec. 1.831(a) is excluded
from the application size fee determination. The provision at 35 U.S.C.
41(a)(1)(G) provides the basis for excluding ``any sequence listing,''
when filed in an electronic medium, from the application size fee
determination. A ``Sequence Listing XML'' is considered as ``any
sequence listing.''
Section 1.52(f)(2)(i) is amended to add a reference to any
``Sequence Listing XML'' in compliance with Sec. 1.831(a).
Section 1.52(f)(3) is amended to add that any ``Sequence Listing
XML'' of 300 MB-800 MB is subject to the surcharge set forth in Sec.
1.21(o)(1) and also add that any ``Sequence Listing XML'' over 800 MB
is subject to the surcharge set forth in Sec. 1.21(o)(2).
Section 1.53: Section 1.53(c)(4) is revised to indicate that a
separate sequence listing in a provisional application disclosing
nucleotide and/or amino acid sequences is not required, but any
biological sequence data submitted in a provisional application filed
on or after July 1, 2022, must be a ``Sequence Listing XML'' in
compliance with Sec. Sec. 1.831 through 1.834. This change does not
apply to provisional applications filed before July 1, 2022.
Section 1.77: Section 1.77(b)(5) is amended to reorganize the
provisions to Sec. 1.77(b)(5)(i) for an incorporation by reference
statement for ASCII plain text files submitted for a ``Computer Program
Listing Appendix'' (Sec. 1.77(b)(5)(i)(A)), a ``Sequence Listing''
(Sec. 1.77(b)(5)(i)(B)), and ``Large Tables'' (Sec.
1.77(b)(5)(i)(C)). Section 1.77(b)(5)(ii) is added to provide for the
provisions for an incorporation by reference statement for a ``Sequence
Listing XML'' submitted via the USPTO patent electronic filing system
or on one or more read-only optical discs.
Section 1.121: Section 1.121(b) is amended to revise the reference
for a ``Sequence Listing'' and eliminate the reference to a CRF of a
``Sequence Listing,'' since a separate CRF (under Sec. 1.821(e)(1) or
(2)) is not part of the specification. The amendment also adds an
exception to amendment practice for a ``Sequence Listing XML'' (Sec.
1.831(a)).
Section 1.121(b)(6) is amended to require that changes to a
``Sequence Listing XML'' be made in accordance with Sec. 1.835.
Section 1.173: The heading of Sec. 1.173(b)(1) is amended to
include `` `Sequence Listing XML' (Sec. 1.831(a)).''
Section 1.173(b)(1)(i) is amended to add an exception to reissue
amendment practice for a `` `Sequence Listing XML' (Sec. 1.831(a)).''
Section 1.173(b)(1)(ii) is amended to provide that changes to a
``Sequence Listing XML'' must be made in accordance with Sec. 1.835.
Section 1.173(d) is amended to add a ``Sequence Listing XML''
(Sec. 1.831(a)) among the items that are excluded from the manner of
making amendments in a reissue application. Reference to specific CFR
provisions for ``Large Tables'' (Sec. 1.58(c)), a ``Computer Program
Listing Appendix'' (Sec. 1.96(c)), and a ``Sequence Listing'' (Sec.
1.821(c)) were added.
Section 1.211: Section 1.211(c) is amended to add a ``Sequence
Listing'' in compliance with Sec. Sec. 1.821 through 1.825 (if
applicable) for an application filed before July 1, 2022, and a
``Sequence Listing XML'' in compliance with Sec. Sec. 1.831 through
1.835 (if applicable) for an application filed on or after July 1,
2022, to the currently listed items that may delay application
publication if not present.
Section 1.495: Section 1.495(c)(5) is amended to delineate between
translations needed for a sequence listing in international
applications entering the national stage in the United States and
having an international filing date before July 1, 2022, and a sequence
listing in XML format for international applications entering the
national stage in the United States and having an international filing
date on or after July 1, 2022. Specifically, the amendment indicates
that a sequence listing need not be translated for national stage entry
if it complies with PCT Rule 12.1(d) and the description complies with
PCT Rule 5.2(b) for applications having an international filing date
before July 1, 2022. However, the amendment indicates that a sequence
listing in XML format must be translated for national stage entry if it
was submitted in an international application having an international
filing date on or after July 1, 2022, with non-English language values
for any language-dependent free text qualifiers. Note that an invention
title is not considered a ``language-dependent free text qualifier''
for purposes of this rule, and translation of the invention title is
not required.
Section 1.495(c)(5), as well as Sec. Sec. 1.833(b)(3) and
1.835(d)(2) as discussed below, were proposed to require that the
``Sequence Listing XML'' contain at least one invention title in
English. This proposal has not been adopted in this final rule. The
proposed requirement for a translation of the title into English was
not adopted in the final rule because applicants in the international
phase need only provide a title in the language of filing, which can be
in a language other than English.
Section 1.530: The heading of Sec. 1.530(d)(1) is amended to
include `` `Sequence Listing XML' (Sec. 1.831(a)).''
Section 1.530(d)(1)(i) is amended to add an exception to
reexamination amendment practice for a `` `Sequence Listing XML' (Sec.
1.831(a)).''
Section 1.530(d)(1)(ii) is amended to provide that changes to a
``Sequence Listing XML'' must be made in accordance with Sec. 1.835.
Section 1.704: Section 1.704(f) is amended to add a ``Sequence
Listing XML'' in compliance with Sec. Sec. 1.831 through 1.835 (if
applicable) to the list of items required for an application filed
under 35 U.S.C. 111(a) to be in condition for examination for purposes
of calculating a reduction in patent term adjustment. The amendment
also adds a ``Sequence Listing XML'' in compliance
[[Page 30812]]
with Sec. Sec. 1.831 through 1.835 (if applicable) to the list of
items that must be submitted in an international application for such
an application to be in condition for examination when the application
has entered the national stage as defined in Sec. 1.491(b). Lastly,
the rule is also amended to add a ``Sequence Listing XML'' in
compliance with Sec. Sec. 1.831 through 1.835 (if applicable) to the
current list of items required for an application to be considered
compliant, for purposes of determining a patent term adjustment
reduction, on the filing date of the latest reply (if any) correcting
the papers, drawings, or ``Sequence Listing'' that is prior to the date
of the mailing of either an action under 35 U.S.C. 132 or a notice of
allowance under 35 U.S.C. 151, whichever occurs first. Lastly, the term
``Sequence Listing'' replaces ``sequence listing,'' since Sec. Sec.
1.821 through 1.825 specifically define a ``Sequence Listing.''
Section 1.831: Section 1.831 is added to provide the heading of
``requirements for patent applications filed on or after July 1, 2022,
having disclosures of nucleotide and/or amino acid sequences.''
Section 1.831(a) is added to specify that patent applications
disclosing nucleotide and/or amino acid sequences by enumeration of
their residues, as defined in paragraph (b) of the section, must
contain, as a separate part of the disclosure, a ``Sequence Listing
XML''. Disclosed nucleotide and/or amino acid sequences that do not
meet the definition in paragraph (b) of the section must not be
included in the ``Sequence Listing XML.'' The ``Sequence Listing XML''
contains information of the nucleotide and/or amino acid sequences
disclosed in the patent application using the symbols and format in
accordance with the requirements of Sec. Sec. 1.832 through 1.834.
Section 1.831(b)(1) and (2) are added to define the nucleotide and
amino acid sequences for which a ``Sequence Listing XML'' is required.
Specifically, nucleotide and/or amino acid sequences, as used in these
rules, encompass: an unbranched sequence or linear region of a branched
sequence containing 4 or more specifically defined amino acids, wherein
the amino acids form a single peptide backbone or an unbranched
sequence or linear region of a branched sequence of 10 or more
specifically defined nucleotides, wherein adjacent nucleotides are
joined by a 3' to 5' (or 5' to 3') phosphodiester linkage or, for
nucleotide analogs, any chemical bond that results in an arrangement of
adjacent nucleobases that mimics the arrangement of nucleobases in
naturally occurring nucleic acids.
Section 1.831(c) is added to state that, where the description or
claims of a patent application discuss a nucleotide and/or amino acid
sequence that is set forth in the ``Sequence Listing XML'' in
accordance with paragraph (a) of the section, reference must be made to
the sequence by use of the sequence identifier, preceded by ``SEQ ID
NO:'' or the like, in the text of the description or claims, even if
the sequence is also embedded in the text of the description or claims
of the patent application. Where a sequence is presented in a drawing,
reference must be made to the sequence by use of the sequence
identifier (Sec. 1.832(a)), either in the drawing or in the Brief
Description of the Drawings, where the correlation between multiple
sequences in the drawing and their sequence identifiers (Sec.
1.832(a)) in the Brief Description is clear. The use of SEQ ID NO: Is
preferred, but including ``or the like'' is intended to ensure that a
formalities notice is not sent when an application uses, for example,
``SEQ NO.'' or ``Seq. Id. No.'' or any similar identification of an
amino acid or nucleotide sequence in the description or claims where it
is clear that a sequence from the ``Sequence Listing XML'' is shown in
the description, claims, or drawings. When identifying the sequence in
the description, claims, or drawings, the numeric sequence identifier
from the ``Sequence Listing XML'' must identify the same sequence.
Section 1.831(d) is added to define the expression ``enumeration of
its residues,'' consistent with the definition in paragraph 3(c)(i) or
(ii) of WIPO Standard ST.26 (incorporated by reference, see 37 CFR
1.839).
Section 1.831(e) is added to define the expression ``specifically
defined,'' consistent with the definition in paragraph 3(k) of WIPO
Standard ST.26.
Section 1.831(f) is added to define the expression ``amino acid,''
consistent with the definition in paragraph 3(a) of WIPO Standard
ST.26.
Section 1.831(g) is added to define the expression ``modified amino
acid,'' consistent with the definition in paragraph 3(e) of WIPO
Standard ST.26.
Section 1.831(h) is added to define the expression ``nucleotide,''
consistent with paragraphs 3(f) and 3(g) of WIPO Standard ST.26.
Section 1.831(i) is added to define the expression ``modified
nucleotide,'' consistent with paragraph 3(f) of WIPO Standard ST.26.
Section 1.831(j) is added to indicate that a ``Sequence Listing
XML'' must not include any sequences having fewer than 10 specifically
defined nucleotides, or fewer than 4 specifically defined amino acids.
Even though Sec. 1.831(a) states that ``[d]isclosed nucleotide or
amino acid sequences that do not meet the definition in paragraph (b)
of this section must not be included in the ``Sequence Listing XML,''
'' adding Sec. 1.831(j) makes explicit the prohibition of including
such sequences in the ``Sequence Listing XML.''
Section 1.832: Section 1.832 is added to provide the manner in
which a nucleotide and/or amino acid sequence is represented in the
``Sequence Listing XML'' part of a patent application having a filing
date on or after July 1, 2022.
Section 1.832(a) is added to define the requirements for the
representation of sequences in the ``Sequence Listing XML'' part of the
application. Specifically, each nucleotide and/or amino acid sequence
represented in the ``Sequence Listing XML'' must be assigned a separate
sequence identifier, and sequence identifiers must begin with the
number 1 and increase sequentially by integers, as defined in paragraph
10 of WIPO Standard ST.26 (incorporated by reference, see 37 CFR
1.839).
Section 1.832(b)(1) through (4) are added to define the
requirements for the representation of nucleotide sequence data in the
``Sequence Listing XML.'' Specifically, a nucleotide sequence must be
represented in the manner described in paragraphs 11-12 of WIPO
Standard ST.26. All nucleotides, including nucleotide analogs, modified
nucleotides, and ``unknown'' nucleotides, within a nucleotide sequence
must be represented and described using symbols in the manner described
in paragraphs 13-19 and 21 of WIPO Standard ST.26. For a region
containing a known number of contiguous ``a,'' ``c,'' ``g,'' ``t,'' or
``n'' residues for which the same description applies, the entire
region may be jointly described as provided in paragraph 22 of WIPO
Standard ST.26.
Section 1.832(c)(1) through (4) are added to define the
requirements for the representation of amino acid sequence data in the
``Sequence Listing XML.'' Specifically, an amino acid sequence must be
represented in the manner described in paragraphs 24 and 25 of WIPO
Standard ST.26. All amino acids, including modified amino acids and
``unknown'' amino acids, within an amino acid sequence must be
represented and described using symbols in the manner described in
paragraphs 26-30 and 32 of WIPO Standard ST.26. For a region containing
a known number of contiguous ``X''
[[Page 30813]]
residues for which the same description applies, the entire region may
be jointly described as provided in paragraph 34 of WIPO Standard
ST.26.
Section 1.832(d) is added to define the manner in which a single
continuous sequence, derived from one or more non-contiguous segments
of a larger sequence, or of segments from different sequences, must be
represented in the ``Sequence Listing XML,'' as described in paragraph
35 of WIPO Standard ST.26.
Section 1.832(e) is added to define the manner in which a
nucleotide and/or amino acid sequence that contains regions of
specifically defined residues separated by one or more regions of
contiguous ``n'' or ``X'' residues of specified length must be
represented in the ``Sequence Listing XML,'' as described in paragraph
36 of WIPO Standard ST.26.
Section 1.832(f) is added to define the manner in which a
nucleotide and/or amino acid sequence that contains regions of
specifically defined residues separated by one or more gaps of an
unknown or undisclosed number of residues must be represented in the
``Sequence Listing XML,'' as described in paragraph 37 of WIPO Standard
ST.26.
Section 1.833: Section 1.833 is added to describe the requirements
for a ``Sequence Listing XML,'' which is required by Sec. 1.831(a) for
disclosures of nucleotides and/or amino acid sequences in patent
applications with a filing date on or after July 1, 2022, to comply
with WIPO Standard ST.26 (incorporated by reference, see 37 CFR 1.839).
Section 1.833(a) is added to require that the ``Sequence Listing
XML'' must be presented as a single XML 1.0 file and encoded using
Unicode UTF-8. Section 1.833(a) also incorporates by reference
paragraphs 40 and 41, and Annex IV of WIPO Standard ST.26 for character
sets.
Section 1.833(b)(1) is added to require that the ``Sequence Listing
XML'' presented in accordance with Sec. 1.833(a) must further be valid
according to the DTD as presented in Annex II of WIPO Standard ST.26.
Section 1.833(b)(2) is added to recite that a ``Sequence Listing
XML'' must comply with the requirements of WIPO Standard ST.26, to
include the items enumerated in Sec. 1.833(b)(2)(i) through (v) as
discussed in the following paragraphs.
Section 1.833(b)(2)(i) is added to require that the ``Sequence
Listing XML'' contain an XML declaration as defined in paragraph 39(a)
of WIPO Standard ST.26.
Section 1.833(b)(2)(ii) is added to require that the ``Sequence
Listing XML'' contain a document type declaration as defined in
paragraph 39(b) of WIPO Standard ST.26.
Section 1.833(b)(2)(iii) is added to require that the ``Sequence
Listing XML'' contain a root element as defined in paragraph 43 of WIPO
Standard ST.26.
Section 1.833(b)(2)(iv) is added to require that the ``Sequence
Listing XML'' contain a general information part that complies with
paragraphs 45, 47, and 48 of WIPO Standard ST.26, as applicable.
Section 1.833(b)(2)(v) is added to require that the ``Sequence
Listing XML'' contain a sequence data part that complies with
paragraphs 50-55, 57, 58, 60-69, 71-78, 80-87, 89-98, and 100 of WIPO
Standard ST.26, as applicable.
Section 1.833(b)(3) is added to require that an INSDQualifier_value
element includes a value for that element in English for each language-
dependent free text qualifier in the ``Sequence Listing XML,'' as
required by Sec. 1.52(b)(1)(ii), and where an INSDQualifier_value
element is defined in paragraphs 76 and 85-87 of WIPO Standard ST.26.
The proposed requirement for a translation of the title into English
was not adopted in the final rule because applicants in the
international phase need only provide a title in the language of
filing, which can be in a language other than English.
Section 1.834: Section 1.834 is added to provide details on the
form and format for nucleotide and/or amino acid sequence submissions
as the ``Sequence Listing XML'' in patent applications filed on or
after July 1, 2022.
Section 1.834(a) is added to indicate that a ``Sequence Listing
XML'' in Unicode UTF-8 created by any means (e.g., text editors,
nucleotide/amino acid sequence editors, or other custom computer
programs) in accordance with Sec. Sec. 1.831 through 1.833 must: (1)
Be compatible with a PC or Mac[supreg] and with MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg]
operating systems; (2) be in XML format, where all permitted printable
characters (including the space character) and non-printable (control)
characters are defined in paragraph 40 of WIPO Standard ST.26
(incorporated by reference, see 37 CFR 1.839); and (3) be named as
*.xml, where ``*'' is one character or a combination of characters
limited to upper- or lowercase letters, numbers, hyphens, and
underscores and the name does not exceed 60 characters in total,
excluding the extension. No spaces or other types of characters are
permitted in the file name.
Section 1.834(b) is added to require that the ``Sequence Listing
XML'' must be in a single file containing the sequence information and
be submitted either: (1) Electronically via the USPTO patent electronic
filing system, where the file size must not exceed 100 MB and file
compression is not permitted; or (2) on read-only optical disc(s) in
compliance with Sec. 1.52(e), where (i) a file that is not compressed
must be contained on a single read-only optical disc, (ii) the file may
be compressed using WinZip[supreg], 7-Zip, or Unix[supreg]/
Linux[supreg] Zip, (iii) a compressed file must not be self-extracting,
and (iv) a compressed XML file that does not fit on a single read-only
optical disc may be split into multiple file parts in accordance with
the target read-only optical disc size and labeled in compliance with
Sec. 1.52(e)(5)(vi).
Section 1.834(c)(1) is added to require that when a ``Sequence
Listing XML'' required by Sec. 1.831(a) is submitted in XML file
format via the USPTO patent electronic filing system or on a read-only
optical disc (in compliance with Sec. 1.52(e)), the specification must
contain a statement in a separate paragraph (see Sec. 1.77(b)(5)) that
incorporates by reference the material in the XML file identifying: (1)
The name of the file, (2) the date of creation, and (3) the size of the
file in bytes, so long as Sec. 1.834(c)(2) does not apply. This
provision was added in the final rule to expressly require an
incorporation by reference statement in the specification to the
``Sequence Listing XML,'' which was only implicitly required by Sec.
1.835(c).
Section 1.834(c)(2) is added to indicate that if the ``Sequence
Listing XML'' required by Sec. 1.831(a) is submitted in XML file
format via the USPTO patent electronic filing system or on a read-only
optical disc (in compliance with Sec. 1.52(e)) for an international
application during the international stage, then an incorporation by
reference statement of the material in the XML file is not required.
This provision was added in the final rule to specifically exempt the
requirement for an incorporation by reference statement in the
specification to the ``Sequence Listing XML'' (as in Sec. 1.834(c)(1))
for a national stage application when the ``Sequence Listing XML''
constituted part of the international application during the
international stage.
Section 1.835: Section 1.835 is added to provide the requirements
for submission of an amendment to add or replace a ``Sequence Listing
XML'' for applications filed on or after July 1, 2022.
[[Page 30814]]
Section 1.835(a) is added to require that any amendment to a patent
application adding an initial submission of a ``Sequence Listing XML''
as required by Sec. 1.831(a) after the application filing date must
include: (1) A ``Sequence Listing XML'' file submitted either (i) via
the USPTO patent electronic filing system, or (ii) on a read-only
optical disc in compliance with Sec. 1.52(e); (2) a request to amend
the specification to include an incorporation by reference statement of
the material in the ``Sequence Listing XML'' file, identifying the name
of the file, the date of creation, and the size of the file in bytes
(see Sec. 1.77(b)(5)(ii)), except when submitted to the United States
International Preliminary Examining Authority for an international
application; (3) a statement that indicates the basis for the
amendment, with specific references to particular parts of the
application as originally filed (specification, claims, drawings) for
all sequence data in the ``Sequence Listing XML''; and (4) a statement
that the ``Sequence Listing XML'' includes no new matter.
Section 1.835(b) is added to require that any amendment adding to,
deleting from, or replacing sequence information in a ``Sequence
Listing XML'' submitted as required by Sec. 1.831(a) must include: (1)
A replacement ``Sequence Listing XML'' containing the entire ``Sequence
Listing XML,'' including any additions, deletions, or replacements of
sequence information, and shall be submitted either (i) via the USPTO
patent electronic filing system, or (ii) on a read-only optical disc,
in compliance with Sec. 1.52(e) labeled as ``REPLACEMENT MM/DD/YYYY''
(with the month, day, and year of creation indicated); (2) an
instruction to amend the specification to include an incorporation by
reference statement of the material in the replacement ``Sequence
Listing XML'' file that identifies the name of the file, the date of
creation, and the size of the file in bytes (see Sec. 1.77(b)(5)(ii)),
except when the replacement ``Sequence Listing XML'' is submitted to
the United States International Preliminary Examining Authority for an
international application; (3) a statement that identifies the location
of all additions, deletions, or replacements of sequence information
relative to the replaced ``Sequence Listing XML''; (4) a statement that
indicates the support for the additions, deletions, or replacements of
the sequence information, with specific references to particular parts
of the application as originally filed (specification, claims,
drawings) for all amended sequence data in the replacement ``Sequence
Listing XML''; and (5) a statement that the replacement ``Sequence
Listing XML'' includes no new matter.
Section 1.835(c) is added to require that the specification of a
complete application with a ``Sequence Listing XML'' as required under
Sec. 1.831(a), present on the application filing date but without an
incorporation by reference of the material contained in the ``Sequence
Listing XML'' file, must be amended to contain a separate paragraph
incorporating by reference the material contained in the ``Sequence
Listing XML'' file, in accordance with Sec. 1.77(b)(5)(ii), except for
international applications.
Section 1.835(d)(1) is added to provide that, when any of the
requirements of Sec. Sec. 1.831 through 1.834 are not satisfied in an
application under 35 U.S.C. 111(a) or in a national stage application
under 35 U.S.C. 371, the applicant will be notified and given a period
of time in which to comply with such requirements to prevent the
abandonment of the application. This final rule indicates that, subject
to Sec. 1.835(d)(2), any amendment to add or replace a ``Sequence
Listing XML'' in response to a requirement under this paragraph must be
submitted in accordance with the requirements of Sec. 1.835(a) through
(c).
Section 1.835(d)(2) is added to explicitly provide that compliance
with Sec. 1.835(a) through (c) is not required for the submission of a
``Sequence Listing XML'' that is solely an English translation of a
previously submitted ``Sequence Listing XML'' that contains non-English
values for any language-dependent free text elements (as per Sec.
1.833(b)(3)). The required submission will be a translated ``Sequence
Listing XML'' in compliance with Sec. Sec. 1.831 through 1.834.
Updated values for attributes in the root element (Sec.
1.833(b)(2)(iii)) or elements of the general information part (Sec.
1.833(b)(2)(iv)) are not considered amendments for purposes of
complying with Sec. 1.835(a) through (c). Even though Sec. Sec.
1.52(b)(1)(ii) and 1.495(c)(1)(i) require a translation for
applications filed under 35 U.S.C. 111(a) and for those entering the
national stage, respectively, this rule makes explicit that when a
translated ``Sequence Listing XML'' is provided as a reply to a notice
that the ``Sequence Listing XML'' contains non-English values for any
language-dependent free text elements, and the translation does not
include the deletion, addition, or replacement of sequence information,
the translated ``Sequence Listing XML'' need not comply with the
requirements for an amended ``Sequence Listing XML'' as set forth in
Sec. 1.835(a) through (c). The proposed requirement for a translation
of the title into English was not adopted in the final rule because
applicants in the international phase need only provide a title in the
language of filing, which can be in a language other than English.
Section 1.835(e) is added to provide that, when any of the
requirements of Sec. Sec. 1.831 through 1.834 are not satisfied at the
time of filing an international application under the PCT, where the
application is to be searched by the United States International
Searching Authority or examined by the United States International
Preliminary Examining Authority, the applicant may be sent a notice
calling for compliance with the requirements within a prescribed time
period. Under PCT Rule 13ter, the applicant may provide, in response to
such a requirement or otherwise, a sequence listing that is a
``Sequence Listing XML'' in accordance with Sec. 1.831(a). The
``Sequence Listing XML'' must be accompanied by a statement that the
information recorded does not go beyond the disclosure in the
international application as filed. In response to such a requirement,
the late furnishing fee set forth in Sec. 1.445(a)(5) is also
required. If the applicant fails to timely provide the required
``Sequence Listing XML,'' the United States International Searching
Authority shall search only to the extent that a meaningful search can
be performed without the ``Sequence Listing XML,'' and the United
States International Preliminary Examining Authority shall examine only
to the extent that a meaningful examination can be performed without
the ``Sequence Listing XML.''
Section 1.835(f) is added to provide that any appropriate
amendments to the ``Sequence Listing XML'' in a patent (e.g., by reason
of reissue, reexamination, or certificate of correction) must comply
with the requirements of paragraph (b) of this section.
Section 1.839: Section 1.839 is added to provide the location of
WIPO Standard ST.26 that is being incorporated by reference.
III. Comments and Responses and Changes From Proposed Rule
The USPTO published a proposed rule on July 6, 2021, at 86 FR
35432, soliciting public comments on the proposed amendments to 37 CFR
part 1 being adopted in this final rule. The USPTO received no comments
from the public on the proposed rule. Even though no comments were
received, the
[[Page 30815]]
proposed changes to Sec. Sec. 1.495(c)(5), 1.833(b)(3) and 1.835(d)(2)
to require a title in English in the ``Sequence Listing XML'' were not
adopted in the final rule. The proposed requirement for a translation
of the title into English was not adopted since applicants in the
international phase need only provide a title in the language of
filing, which can be in a language other than English. Additionally,
even though Sec. 1.831(a) states that ``[d]isclosed nucleotide or
amino acid sequences that do not meet the definition in paragraph (b)
of this section must not be included in the ``Sequence Listing XML,''
'' Sec. 1.831(j) was added to make explicit the prohibition of
including such sequences in the ``Sequence Listing XML.'' Section
1.834(c)(1) was added to expressly require an incorporation by
reference statement in the specification to the ``Sequence Listing
XML,'' which was only implicitly required by Sec. 1.835(c). Lastly,
Sec. 1.834(c)(2) was added to specifically exempt the requirement for
an incorporation by reference statement in the specification to the
``Sequence Listing XML'' (as in Sec. 1.834(c)(1)) for a national stage
application when the ``Sequence Listing XML'' constituted part of the
international application during the international stage.
IV. Rulemaking Considerations
A. Administrative Procedure Act: The changes in this rulemaking
involve rules of agency practice and procedure, and/or interpretive
rules. See Bachow Commc'ns Inc. v. FCC, 237 F.3d 683, 690 (D.C. Cir.
2001) (changes to procedural rules are not subject to notice and
comment review under the Administrative Procedure Act (APA)); Inova
Alexandria Hosp. v. Shalala, 244 F.3d 342, 349 (4th Cir. 2001) (rules
for handling appeals are procedural where they do not change the
substantive standard for reviewing claims); Nat'l Org. of Veterans'
Advocates v. Sec'y of Veterans Affairs, 260 F.3d 1365, 1375 (Fed. Cir.
2001) (Substantive rules ``effect a change in existing law or policy or
which affect individual rights and obligations,'' whereas
interpretative rules ``clarify or explain existing law or regulation
and are exempt from notice and comment'' review under the APA.).
Accordingly, prior notice and opportunity for public comment for
the changes in this rulemaking were not required pursuant to 5 U.S.C.
553(b) or (c), or any other law. See Cooper Techs. Co. v. Dudas, 536
F.3d 1330, 1336-37 (Fed. Cir. 2008) (stating that 5 U.S.C. 553, and
thus 35 U.S.C. 2(b)(2)(B), do not require notice and comment rulemaking
for ``interpretative rules, general statements of policy, or rules of
agency organization, procedure, or practice'' (quoting 5 U.S.C.
553(b)(A))). However, the USPTO chose to seek public comment before
implementing the rule to benefit from the public's input.
B. Regulatory Flexibility Act: For the reasons set forth in this
notice, the Senior Counsel for Regulatory and Legislative Affairs of
the USPTO has certified to the Chief Counsel for Advocacy of the Small
Business Administration that this rule will not have a significant
economic impact on a substantial number of small entities. See 5 U.S.C.
605(b).
The USPTO amends the rules of practice to require the submission of
biological sequence data in XML where the rules of practice incorporate
by reference WIPO Standard ST.26, ``Recommended Standard for the
Presentation of Nucleotide and Amino Acid Sequence Listings Using XML
(eXtensible Markup Language),'' including Annexes I-VII, version 1.5,
approved November 5, 2021, as disclosed in the WIPO Handbook on
Industrial Property Information and Documentation.
This rulemaking makes more technical data associated with
biotechnology inventions available to the public because the new rules
of practice based on WIPO Standard ST.26 provide for enhanced
biological sequence data related to disclosures of nucleotide and/or
amino acid sequences in patent applications. WIPO Standard ST.26
provides clear rules as to what must be included in a sequence listing
and how sequences must be represented (e.g., standardization of the
representation of modified nucleic acids and amino acids as well as
variants derived from primary sequences). WIPO Standard ST.26 contains
a guidance document that demonstrates the requirement for inclusion and
representation of biological sequence data. As a result, patent
applicants will have a clearer understanding as to the requirements and
presentation of biological sequence data in a compliant sequence
listing under WIPO Standard ST.26. Additionally, since WIPO Standard
ST.26 only allows XML format, applicants will not be burdened with or
confused by the requirements of filing a sequence listing in paper or
PDF format, and IPOs will not be burdened with processing paper
sequence listings and performing necessary checks on the contents of
the paper documents. The changes in this rulemaking are largely
procedural in nature, and do not impose any additional requirements or
fees on applicants. For the foregoing reasons, the changes in this rule
will not have a significant economic impact on a substantial number of
small entities.
C. Executive Order 12866 (Regulatory Planning and Review): This
rulemaking has been determined to be not significant for purposes of
Executive Order 12866 (Sept. 30, 1993).
D. Executive Order 13563 (Improving Regulation and Regulatory
Review): The USPTO has complied with Executive Order 13563 (Jan. 18,
2011). Specifically, to the extent feasible and applicable, the USPTO
has: (1) Reasonably determined that the benefits of the rule justify
its costs; (2) tailored the rule to impose the least burden on society
consistent with obtaining the agency's regulatory objectives; (3)
selected a regulatory approach that maximizes net benefits; (4)
specified performance objectives; (5) identified and assessed available
alternatives; (6) involved the public in an open exchange of
information and perspectives among experts in relevant disciplines,
affected stakeholders in the private sector, and the public as a whole,
and provided online access to the rulemaking docket; (7) attempted to
promote coordination, simplification, and harmonization across
government agencies and identified goals designed to promote
innovation; (8) considered approaches that reduce burdens while
maintaining flexibility and freedom of choice for the public; and (9)
ensured the objectivity of scientific and technological information and
processes.
E. Executive Order 13132 (Federalism): This rulemaking does not
contain policies with federalism implications sufficient to warrant
preparation of a Federalism Assessment under Executive Order 13132
(Aug. 4, 1999).
F. Executive Order 13175 (Tribal Consultation): This rulemaking
will not: (1) Have substantial direct effects on one or more Indian
tribes; (2) impose substantial direct compliance costs on Indian tribal
governments; or (3) preempt tribal law. Therefore, a tribal summary
impact statement is not required under Executive Order 13175 (Nov. 6,
2000).
G. Executive Order 13211 (Energy Effects): This rulemaking is not a
significant energy action under Executive Order 13211 because this
rulemaking is not likely to have a significant adverse effect on the
supply, distribution, or use of energy. Therefore, a Statement of
Energy Effects is not required under Executive Order 13211 (May 18,
2001).
H. Executive Order 12988 (Civil Justice Reform): This rulemaking
meets applicable standards to minimize
[[Page 30816]]
litigation, eliminate ambiguity, and reduce burden as set forth in
sections 3(a) and 3(b)(2) of Executive Order 12988 (Feb. 5, 1996).
I. Executive Order 13045 (Protection of Children): This rulemaking
does not concern an environmental risk to health or safety that may
disproportionately affect children under Executive Order 13045 (Apr.
21, 1997).
J. Executive Order 12630 (Taking of Private Property): This
rulemaking will not affect a taking of private property or otherwise
have taking implications under Executive Order 12630 (Mar. 15, 1988).
K. Congressional Review Act: Under the Congressional Review Act
provisions of the Small Business Regulatory Enforcement Fairness Act of
1996 (5 U.S.C. 801 et seq.), the USPTO will submit a report containing
the final rule and other required information to the United States
Senate, the United States House of Representatives, and the Comptroller
General of the Government Accountability Office. The changes in this
rulemaking are not expected to result in an annual effect on the
economy of $100 million or more, a major increase in costs or prices,
or significant adverse effects on competition, employment, investment,
productivity, innovation, or the ability of United States-based
enterprises to compete with foreign-based enterprises in domestic and
export markets. Therefore, this rulemaking is not expected to result in
a ``major rule'' as defined in 5 U.S.C. 804(2).
L. Unfunded Mandates Reform Act of 1995: The changes set forth in
this rulemaking do not involve a Federal intergovernmental mandate that
will result in the expenditure by State, local, and tribal governments,
in the aggregate, of $100 million (as adjusted) or more in any one
year, or a Federal private sector mandate that will result in the
expenditure by the private sector of $100 million (as adjusted) or more
in any one year, and will not significantly or uniquely affect small
governments. Therefore, no actions are necessary under the provisions
of the Unfunded Mandates Reform Act of 1995. See 2 U.S.C. 1501 et seq.
M. National Environmental Policy Act of 1969: This rulemaking will
not have any effect on the quality of the environment and is thus
categorically excluded from review under the National Environmental
Policy Act of 1969. See 42 U.S.C. 4321 et seq.
N. National Technology Transfer and Advancement Act of 1995: The
requirements of section 12(d) of the National Technology Transfer and
Advancement Act of 1995 (15 U.S.C. 272 note) are not applicable because
this rulemaking does not contain provisions that involve the use of
technical standards.
O. Paperwork Reduction Act of 1995: The Paperwork Reduction Act of
1995 (44 U.S.C. 3501-3549) requires that the USPTO consider the impact
of paperwork and other information collection burdens imposed on the
public. In accordance with section 3507(d) of the Paperwork Reduction
Act of 1995, the majority of the paperwork and other information
collection burdens discussed in this rule have already been approved
under the following Office of Management and Budget (OMB) Control
Numbers: 0651-0024 (Sequence Listing), 0651-0031 (Patent Processing),
0651-0032 (Initial Patent Applications), and 0651-0064 (Patent
Reexaminations and Supplemental Examinations).
Modifications to 0651-0024 because of this rulemaking will be
submitted to OMB for approval. Modifications include the removal of the
Sequence Listing in Application (paper), which will result in an
estimated reduction in the burden associated with this information
collection by 5,000 responses and 30,000 burden hours. These burden
estimates are based on the current OMB approved burdens (response
volumes) associated with this information collection, which may be
different from any forecasts mentioned in other parts of this rule.
The changes discussed in this rule do not affect the information
collection requirements or burdens associated with 0651-0031, 0651-
0032, and 0651-0064 listed above; therefore, the USPTO does not plan to
take any additional actions on these information collections as a
result of this rulemaking. 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 has a currently valid OMB control number.
P. E-Government Act Compliance: The USPTO is committed to
compliance with the E-Government Act to promote the use of the internet
and other information technologies, to provide increased opportunities
for citizen access to Government information and services, and for
other purposes.
List of Subjects in 37 CFR Part 1
Administrative practice and procedure, Biologics, Courts, Freedom
of information, Incorporation by reference, Inventions and patents,
Reporting and recordkeeping requirements, Small businesses.
For the reasons stated in the preamble and under the authority
contained in 35 U.S.C. 2, as amended, the USPTO amends 37 CFR part 1 as
follows:
PART 1--RULES OF PRACTICE IN PATENT CASES
0
1. The authority citation for part 1 continues to read as follows:
Authority: 35 U.S.C. 2(b)(2), unless otherwise noted.
0
2. Section 1.52 is amended by:
0
a. Revising paragraphs (e)(1)(ii) and (e)(3)(ii) and (iii);
0
b. Adding paragraph (e)(3)(iv); and
0
c. Revising paragraphs (e)(7), (f)(1) introductory text, (f)(1)(i),
(f)(2) introductory text, (f)(2)(i), and (f)(3).
The revisions and addition read as follows:
Sec. 1.52 Language, paper, writing, margins, read-only optical disc
specifications.
* * * * *
(e) * * *
(1) * * *
(ii) A ``Sequence Listing'' (submitted under Sec. 1.821(c) in
compliance with Sec. Sec. 1.822 through 1.824) or a ``Sequence Listing
XML'' (submitted under Sec. 1.831(a) in compliance with Sec. Sec.
1.832 through 1.834); or
* * * * *
(3) * * *
(ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], MacOS[supreg], or Unix[supreg]/Linux[supreg];
(iii) The contents of each read-only optical disc must be in
American Standard Code for Information Interchange (ASCII) plain text
and if compressed, must be compressed in accordance with Sec. 1.58 for
``Large Tables,'' with Sec. 1.96 for a ``Computer Program Listing
Appendix,'' or Sec. 1.824 for a ``Sequence Listing'' or Computer
Readable Form (CRF) of the ``Sequence Listing,'' as applicable; and
(iv) The contents of each read-only optical disc for a ``Sequence
Listing XML'' must be in eXtensible Markup Language (XML) file format,
and if compressed, must be compressed in accordance with Sec. 1.834.
* * * * *
(7) Any amendment to the information on a read-only optical disc
must be by way of a replacement read-only optical disc, in compliance
with Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a
``Computer Program Listing Appendix,'' Sec. 1.825(b) for a ``Sequence
Listing'' or CRF of a ``Sequence Listing,'' and Sec. 1.835(b) for a
``Sequence Listing XML.''
* * * * *
[[Page 30817]]
(f) * * *
(1) Submission on read-only optical discs. The application size fee
required by Sec. 1.16(s) or Sec. 1.492(j), for an application
component submitted in part on a read-only optical disc in compliance
with paragraph (e) of this section, shall be determined such that each
three kilobytes of content submitted on a read-only optical disc shall
be counted as a sheet of paper. Excluded from this determination is any
ASCII plain text file or any XML file (as applicable) submitted on a
read-only optical disc under paragraph (e) of this section containing:
(i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing'' in
compliance with Sec. 1.821(c) or (e), or any ``Sequence Listing XML''
in compliance with Sec. 1.831(a); or
* * * * *
(2) Submission via the USPTO patent electronic filing system. The
application size fee required by Sec. 1.16(s) or Sec. 1.492(j), for
an application submitted in whole or in part via the USPTO patent
electronic filing system, shall be determined such that the paper size
equivalent will be considered to be 75% of the number of sheets of
paper present in the specification and drawings for the application
when entered into the Office records after being rendered by the USPTO
patent electronic filing system. Excluded from this determination is
any ASCII plain text file or any XML file (as applicable) submitted via
the USPTO patent electronic filing system containing:
(i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing'' in
compliance with Sec. 1.821(c)(1) or (e), or any ``Sequence Listing
XML'' in compliance with Sec. 1.831(a); or
* * * * *
(3) Oversized submission. Any submission of a ``Sequence Listing''
in electronic form or a ``Sequence Listing XML'' of 300 MB-800 MB filed
in an application under 35 U.S.C. 111 or 371 will be subject to the fee
set forth in Sec. 1.21(o)(1). Any submission of a ``Sequence Listing''
in electronic form or a ``Sequence Listing XML'' that exceeds 800 MB
filed in an application under 35 U.S.C. 111 or 371 will be subject to
the fee set forth in Sec. 1.21(o)(2).
0
3. Section 1.53 is amended by revising paragraph (c)(4) to read as
follows:
Sec. 1.53 Application number, filing date, and completion of
application.
* * * * *
(c) * * *
(4) A provisional application is not entitled to the right of
priority under 35 U.S.C. 119, 365(a), or 386(a) or Sec. 1.55, or to
the benefit of an earlier filing date under 35 U.S.C. 120, 121, 365(c),
or 386(c) or Sec. 1.78 of any other application. No claim for priority
under 35 U.S.C. 119(e) or Sec. 1.78(a) may be made in a design
application based on a provisional application. A provisional
application disclosing nucleotide and/or amino acid sequences is not
required to include a separate sequence listing; however, if submitted
in a provisional application filed on or after July 1, 2022, any
submission of nucleotide and/or amino acid sequence data must be by way
of a ``Sequence Listing XML'' in compliance with Sec. Sec. 1.831
through 1.834.
* * * * *
0
4. Section 1.77 is amended by revising paragraph (b)(5) to read as
follows:
Sec. 1.77 Arrangement of application elements.
* * * * *
(b) * * *
(5) An incorporation by reference statement regarding the material
in:
(i) One or more ASCII plain text files, submitted via the USPTO
patent electronic filing system or on one or more read-only optical
discs (see Sec. 1.52(e)(8)), identifying the names of each file, the
date of creation of each file, and the size of each file in bytes, for
the following document types:
(A) A ``Computer Program Listing Appendix'' (see Sec. 1.96(c));
(B) A ``Sequence Listing'' (see Sec. 1.821(c)); or
(C) ``Large Tables'' (see Sec. 1.58(c)).
(ii) An XML file for a ``Sequence Listing XML'' (see Sec.
1.831(a)), submitted via the USPTO patent electronic filing system or
on one or more read-only optical discs (see Sec. 1.52(e)(8)),
identifying the names of each file, the date of creation of each file,
and the size of each file in bytes.
* * * * *
0
5. Section 1.121 is amended by revising paragraphs (b) introductory
text and (b)(6) to read as follows:
Sec. 1.121 Manner of making amendments in applications.
* * * * *
(b) Specification. Amendments to the specification, other than the
claims, ``Large Tables'' (Sec. 1.58(c)), a ``Computer Program Listing
Appendix'' (Sec. 1.96(c)(5) and (7)), a ``Sequence Listing'' (Sec.
1.825), or a ``Sequence Listing XML'' (Sec. 1.835), must be made by
adding, deleting, or replacing a paragraph; by replacing a section; or
by providing a substitute specification, in the manner specified in
this section.
* * * * *
(6) Amendments to ``Large Tables,'' a ``Computer Program Listing
Appendix,'' a ``Sequence Listing,'' or a ``Sequence Listing XML.''
Changes to ``Large Tables,'' a ``Computer Program Listing Appendix,'' a
``Sequence Listing,'' or a ``Sequence Listing XML'' must be made in
accordance with Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5)
for a ``Computer Program Listing Appendix,'' Sec. 1.825 for a
``Sequence Listing,'' or Sec. 1.835 for a ``Sequence Listing XML.''
* * * * *
0
6. Section 1.173 is amended by revising paragraphs (b)(1) and (d)
introductory text to read as follows:
Sec. 1.173 Reissue specification, drawings, and amendments.
* * * * *
(b) * * *
(1) Specification other than the claims, ``Large Tables'' (Sec.
1.58(c)), a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), a
``Sequence Listing'' (Sec. 1.821(c)), or a ``Sequence Listing XML''
(Sec. 1.831(a)). (i) Changes to the specification, other than to the
claims, ``Large Tables'' (Sec. 1.58(c)), a ``Computer Program Listing
Appendix'' (Sec. 1.96(c)), a ``Sequence Listing'' (Sec. 1.821(c)), or
a ``Sequence Listing XML'' (Sec. 1.831(a)), must be made by submission
of the entire text of an added or rewritten paragraph, including
markings pursuant to paragraph (d) of this section, except that an
entire paragraph may be deleted by a statement deleting the paragraph,
without presentation of the text of the paragraph. The precise point in
the specification where any added or rewritten paragraph is located
must be identified.
(ii) Changes to ``Large Tables,'' a ``Computer Program Listing
Appendix,'' a ``Sequence Listing,'' or a ``Sequence Listing XML'' must
be made in accordance with Sec. 1.58(g) for ``Large Tables,'' Sec.
1.96(c)(5) for a ``Computer Program Listing Appendix,'' Sec. 1.825 for
a ``Sequence Listing,'' and Sec. 1.835 for a ``Sequence Listing XML.''
* * * * *
(d) Changes shown by markings. Any changes relative to the patent
being reissued that are made to the specification, including the claims
but excluding ``Large Tables'' (Sec. 1.58(c)), a ``Computer Program
Listing Appendix'' (Sec. 1.96(c)), a ``Sequence Listing'' (Sec.
1.821(c)), and a ``Sequence Listing XML'' (Sec. 1.831(a)) upon filing
or by an amendment paper in the reissue application, must include the
following markings:
* * * * *
0
7. Section 1.211 is amended by revising paragraph (c) to read as
follows:
[[Page 30818]]
Sec. 1.211 Publication of applications.
* * * * *
(c) An application filed under 35 U.S.C. 111(a) will not be
published until it includes the basic filing fee (Sec. 1.16(a) or (c))
and any English translation required by Sec. 1.52(d). The Office may
delay publishing any application until it includes any application size
fee required by the Office under Sec. 1.16(s) or Sec. 1.492(j), a
specification having papers in compliance with Sec. 1.52 and an
abstract (Sec. 1.72(b)), drawings in compliance with Sec. 1.84, a
``Sequence Listing'' in compliance with Sec. Sec. 1.821 through 1.825
(if applicable) for an application filed before July 1, 2022, a
``Sequence Listing XML'' in compliance with Sec. Sec. 1.831 through
1.835 (if applicable) for an application filed on or after July 1,
2022, and the inventor's oath or declaration or application data sheet
containing the information specified in Sec. 1.63(b).
* * * * *
0
8. Section 1.495 is amended by revising paragraph (c)(5) to read as
follows:
Sec. 1.495 Entering the national stage in the United States of
America.
* * * * *
(c) * * *
(5) For international applications having an international filing
date before July 1, 2022, a sequence listing need not be translated if
the sequence listing complies with PCT Rule 12.1(d) and the description
complies with PCT Rule 5.2(b). For international applications having an
international filing date on or after July 1, 2022, for purposes of
paragraph (c)(1)(i) of this section, an English translation is required
for any sequence listing in XML format (``Sequence Listing XML'')
containing non-English language values for any language-dependent free
text qualifiers in accordance with Sec. Sec. 1.831 through 1.834.
* * * * *
0
9. Section 1.530 is amended by revising paragraph (d)(1) to read as
follows:
Sec. 1.530 Statement by patent owner in ex parte reexamination;
amendment by patent owner in ex parte or inter partes reexamination;
inventorship change in ex parte or inter partes reexamination.
* * * * *
(d) * * *
(1) Specification other than the claims, ``Large Tables'' (Sec.
1.58(c)), a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), a
``Sequence Listing'' (Sec. 1.821(c)), or a ``Sequence Listing XML
(Sec. 1.831(a)). (i) Changes to the specification, other than to the
claims, ``Large Tables'' (Sec. 1.58(c)), a ``Computer Program Listing
Appendix'' (Sec. 1.96(c)), a ``Sequence Listing'' (Sec. 1.821(c)), or
a ``Sequence Listing XML'' (Sec. 1.831(a)), must be made by submission
of the entire text of an added or rewritten paragraph, including
markings pursuant to paragraph (f) of this section, except that an
entire paragraph may be deleted by a statement deleting the paragraph,
without presentation of the text of the paragraph. The precise point in
the specification where any added or rewritten paragraph is located
must be identified.
(ii) Changes to ``Large Tables,'' a ``Computer Program Listing
Appendix,'' a ``Sequence Listing,'' or a ``Sequence Listing XML'' must
be made in accordance with Sec. 1.58(g) for ``Large Tables,'' Sec.
1.96(c)(5) for a ``Computer Program Listing Appendix,'' Sec. 1.825 for
a ``Sequence Listing,'' or Sec. 1.835 for a ``Sequence Listing XML.''
* * * * *
0
10. Section 1.704 is amended by revising paragraph (f) to read as
follows:
Sec. 1.704 Reduction of period of adjustment of patent term.
* * * * *
(f) An application filed under 35 U.S.C. 111(a) is in condition for
examination when it includes a specification, including at least one
claim and an abstract (Sec. 1.72(b)), and has papers in compliance
with Sec. 1.52, drawings (if any) in compliance with Sec. 1.84, any
English translation required by Sec. 1.52(d) or Sec. 1.57(a), a
``Sequence Listing'' in compliance with Sec. Sec. 1.821 through 1.825
(if applicable), a ``Sequence Listing XML'' in compliance with
Sec. Sec. 1.831 through 1.835 (if applicable), an inventor's oath or
declaration or an application data sheet containing the information
specified in Sec. 1.63(b), the basic filing fee (Sec. 1.16(a) or
(c)), the search fee (Sec. 1.16(k) or (m)), the examination fee (Sec.
1.16(o) or (q)), any certified copy of the previously filed application
required by Sec. 1.57(a), and any application size fee required by the
Office under Sec. 1.16(s). An international application is in
condition for examination when it has entered the national stage as
defined in Sec. 1.491(b), and includes a specification, including at
least one claim and an abstract (Sec. 1.72(b)), and has papers in
compliance with Sec. 1.52, drawings (if any) in compliance with Sec.
1.84, a ``Sequence Listing'' in compliance with Sec. Sec. 1.821
through 1.825 (if applicable), a ``Sequence Listing XML'' in compliance
with Sec. Sec. 1.831 through 1.835 (if applicable), an inventor's oath
or declaration or an application data sheet containing the information
specified in Sec. 1.63(b), the search fee (Sec. 1.492(b)), the
examination fee (Sec. 1.492(c)), and any application size fee required
by the Office under Sec. 1.492(j). An application shall be considered
as having papers in compliance with Sec. 1.52, drawings (if any) in
compliance with Sec. 1.84, and a ``Sequence Listing'' in compliance
with Sec. Sec. 1.821 through 1.825 (if applicable), or a ``Sequence
Listing XML'' in compliance with Sec. Sec. 1.831 through 1.835 (if
applicable), for purposes of this paragraph (f) on the filing date of
the latest reply (if any) correcting the papers, drawings, ``Sequence
Listing,'' or ``Sequence Listing XML'' that is prior to the date of
mailing of either an action under 35 U.S.C. 132 or a notice of
allowance under 35 U.S.C. 151, whichever occurs first.
0
11. Sections 1.831 through 1.835 and 1.839 are added to read as
follows:
Sec.
* * * * *
1.831 Requirements for patent applications filed on or after July 1,
2022, having nucleotide and/or amino acid sequence disclosures.
1.832 Representation of nucleotide and/or amino acid sequence data
in the ``Sequence Listing XML'' part of a patent application filed
on or after July 1, 2022.
1.833 Requirements for a ``Sequence Listing XML'' for nucleotide
and/or amino acid sequences as part of a patent application filed on
or after July 1, 2022.
1.834 Form and format for nucleotide and/or amino acid sequence
submissions as the ``Sequence Listing XML'' in patent applications
filed on or after July 1, 2022.
1.835 Amendment to add or replace a ``Sequence Listing XML'' in
patent applications filed on or after July 1, 2022.
1.839 Incorporation by reference.
* * * * *
Sec. 1.831 Requirements for patent applications filed on or after
July 1, 2022, having nucleotide and/or amino acid sequence disclosures.
(a) Patent applications disclosing nucleotide and/or amino acid
sequences by enumeration of their residues, as defined in paragraph (b)
of this section, must contain, as a separate part of the disclosure, a
computer readable Sequence Listing in XML format (a ``Sequence Listing
XML''). Disclosed nucleotide or amino acid sequences that do not meet
the definition in paragraph (b) of this section must not be included in
the ``Sequence Listing XML.'' The ``Sequence Listing XML'' contains the
information of the nucleotide and/or amino acid sequences disclosed in
the patent application using the symbols and format in accordance with
the requirements of Sec. Sec. 1.832 through 1.834.
[[Page 30819]]
(b) Nucleotide and/or amino acid sequences, as used in this section
and Sec. Sec. 1.832 through 1.835, encompass:
(1) An unbranched sequence or linear region of a branched sequence
containing 4 or more specifically defined amino acids, wherein the
amino acids form a single peptide backbone; or
(2) An unbranched sequence or linear region of a branched sequence
of 10 or more specifically defined nucleotides, wherein adjacent
nucleotides are joined by:
(i) A 3' to 5' (or 5' to 3') phosphodiester linkage; or
(ii) Any chemical bond that results in an arrangement of adjacent
nucleobases that mimics the arrangement of nucleobases in naturally
occurring nucleic acids (i.e., nucleotide analogs).
(c) Where the description or claims of a patent application discuss
a sequence that is set forth in the ``Sequence Listing XML'' in
accordance with paragraph (a) of this section, reference must be made
to the sequence by use of the sequence identifier, preceded by ``SEQ ID
NO:'' or the like in the text of the description or claims, even if the
sequence is also embedded in the text of the description or claims of
the patent application. Where a sequence is presented in a drawing,
reference must be made to the sequence by use of the sequence
identifier (Sec. 1.832(a)), either in the drawing or in the Brief
Description of the Drawings, where the correlation between multiple
sequences in the drawing and their sequence identifiers (Sec.
1.832(a)) in the Brief Description is clear.
(d) ``Enumeration of its residues'' means disclosure of a
nucleotide or amino acid sequence in a patent application by listing,
in order, each residue of the sequence, where the residues are
represented in the manner as defined in paragraph 3(c)(i) or (ii) of
WIPO Standard ST.26 (incorporated by reference, see Sec. 1.839).
(e) ``Specifically defined'' means any amino acid or nucleotide as
defined in paragraph 3(k) of WIPO Standard ST.26.
(f) ``Amino acid'' includes any D- or L-amino acid or modified
amino acid as defined in paragraph 3(a) of WIPO Standard ST.26.
(g) ``Modified amino acid'' includes any amino acid as described in
paragraph 3(e) of WIPO Standard ST.26.
(h) ``Nucleotide'' includes any nucleotide, nucleotide analog, or
modified nucleotide as defined in paragraphs 3(f) and 3(g) of WIPO
Standard ST.26.
(i) ``Modified nucleotide'' includes any nucleotide as described in
paragraph 3(f) of WIPO Standard ST.26.
(j) A ``Sequence listing XML'' must not include any sequences
having fewer than 10 specifically defined nucleotides, or fewer than 4
specifically defined amino acids.
Sec. 1.832 Representation of nucleotide and/or amino acid sequence
data in the ``Sequence Listing XML'' part of a patent application filed
on or after July 1, 2022.
(a) Each disclosed nucleotide or amino acid sequence that meets the
requirements of Sec. 1.831(b) must appear separately in the ``Sequence
Listing XML.'' Each sequence set forth in the ``Sequence Listing XML''
must be assigned a separate sequence identifier. The sequence
identifiers must begin with 1 and increase sequentially by integers as
defined in paragraph 10 of WIPO Standard ST.26 (incorporated by
reference, see Sec. 1.839).
(b) The representation and symbols for nucleotide sequence data
shall conform to the requirements of paragraphs (b)(1) through (4) of
this section.
(1) A nucleotide sequence must be represented in the manner
described in paragraphs 11-12 of WIPO Standard ST.26.
(2) All nucleotides, including nucleotide analogs, modified
nucleotides, and ``unknown'' nucleotides, within a nucleotide sequence
must be represented using the symbols set forth in paragraphs 13-16,
19, and 21 of WIPO Standard ST.26.
(3) Modified nucleotides within a nucleotide sequence must be
described in the manner discussed in paragraphs 17, 18, and 19 of WIPO
Standard ST.26.
(4) A region containing a known number of contiguous ``a,'' ``c,''
``g,'' ``t,'' or ``n'' residues for which the same description applies
may be jointly described in the manner described in paragraph 22 of
WIPO Standard ST.26.
(c) The representation and symbols for amino acid sequence data
shall conform to the requirements of paragraphs (c)(1) through (4) of
this section.
(1) The amino acids in an amino acid sequence must be represented
in the manner described in paragraphs 24 and 25 of WIPO Standard ST.26.
(2) All amino acids, including modified amino acids and ``unknown''
amino acids, within an amino acid sequence must be represented using
the symbols set forth in paragraphs 26-29 and 32 of WIPO Standard
ST.26.
(3) Modified amino acids within an amino acid sequence must be
described in the manner discussed in paragraphs 29 and 30 of WIPO
Standard ST.26.
(4) A region containing a known number of contiguous ``X'' residues
for which the same description applies may be jointly described in the
manner described in paragraph 34 of WIPO Standard ST.26.
(d) A nucleotide and/or amino acid sequence that is constructed as
a single continuous sequence derived from one or more non-contiguous
segments of a larger sequence or of segments from different sequences
must be listed in the ``Sequence Listing XML'' in the manner described
in paragraph 35 of WIPO Standard ST.26.
(e) A nucleotide and/or amino acid sequence that contains regions
of specifically defined residues separated by one or more regions of
contiguous ``n'' or ``X'' residues, wherein the exact number of ``n''
or ``X'' residues in each region is disclosed, must be listed in the
``Sequence Listing XML'' in the manner described in paragraph 36 of
WIPO Standard ST.26.
(f) A nucleotide and/or amino acid sequence that contains regions
of specifically defined residues separated by one or more gaps of an
unknown or undisclosed number of residues must be listed in the
``Sequence Listing XML'' in the manner described in paragraph 37 of
WIPO Standard ST.26.
Sec. 1.833 Requirements for a ``Sequence Listing XML'' for
nucleotide and/or amino acid sequences as part of a patent application
filed on or after July 1, 2022.
(a) The ``Sequence Listing XML'' as required by Sec. 1.831(a) must
be presented as a single file in XML 1.0 encoded using Unicode UTF-8,
where the character set complies with paragraphs 40 and 41 and Annex IV
of WIPO Standard ST.26 (incorporated by reference, see Sec. 1.839).
(b) The ``Sequence Listing XML'' presented in accordance with
paragraph (a) of this section must further:
(1) Be valid according to the Document Type Definition (DTD) as
presented in WIPO Standard ST.26, Annex II.
(2) Comply with the requirements of WIPO Standard ST.26 to include:
(i) An XML declaration as defined in paragraph 39(a) of WIPO
Standard ST.26;
(ii) A document type (DOCTYPE) declaration as defined in paragraph
39(b) of WIPO Standard ST.26;
(iii) A root element as defined in paragraph 43 of WIPO Standard
ST.26;
(iv) A general information part that complies with the requirements
of paragraphs 45, 47, and 48, as applicable, of WIPO Standard ST.26;
and
(v) A sequence data part that complies with the requirements of
paragraphs 50-55, 57, 58, 60-69, 71-78, 80-87, 89-98, and 100, as
applicable, of WIPO
[[Page 30820]]
Standard ST.26 representing the nucleotide and/or amino acid sequences
according to Sec. 1.832.
(3) Include an INSDQualifier_value element with a value in English
for any language-dependent free text qualifier as defined by paragraphs
76 and 85-87 of WIPO Standard ST.26, and as required by Sec.
1.52(b)(1)(ii).
Sec. 1.834 Form and format for nucleotide and/or amino acid sequence
submissions as the ``Sequence Listing XML'' in patent applications
filed on or after July 1, 2022.
(a) A ``Sequence Listing XML'' encoded using Unicode UTF-8, created
by any means (e.g., text editors, nucleotide/amino acid sequence
editors, or other custom computer programs) in accordance with
Sec. Sec. 1.831 through 1.833, must:
(1) Have the following compatibilities:
(i) Computer compatibility: PC or Mac[supreg]; and
(ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg].
(2) Be in XML format, where all permitted printable characters
(including the space character) and non-printable (control) characters
are defined in paragraph 40 of WIPO Standard ST.26 (incorporated by
reference, see Sec. 1.839).
(3) Be named as *.xml, where ``*'' is one character or a
combination of characters limited to upper- or lowercase letters,
numbers, hyphens, and underscores, and the name does not exceed 60
characters in total, excluding the extension. No spaces or other types
of characters are permitted in the file name.
(b) The ``Sequence Listing XML'' must be in a single file
containing the sequence information and be submitted either:
(1) Electronically via the USPTO patent electronic filing system,
where the file size must not exceed 100 MB, and file compression is not
permitted; or
(2) On read-only optical disc(s) in compliance with Sec. 1.52(e),
where:
(i) A file that is not compressed must be contained on a single
read-only optical disc;
(ii) The file may be compressed using WinZip[supreg], 7-Zip, or
Unix[supreg]/Linux[supreg] Zip;
(iii) A compressed file must not be self-extracting; or
(iv) A compressed XML file that does not fit on a single read-only
optical disc may be split into multiple file parts, in accordance with
the target read-only optical disc size, and labeled in compliance with
Sec. 1.52(e)(5)(vi);
(c)(1) Unless paragraph (c)(2) of this section applies, when the
``Sequence Listing XML'' required by Sec. 1.831(a) is submitted in XML
file format via the USPTO patent electronic filing system or on a read-
only optical disc (in compliance with Sec. 1.52(e)), then the
specification must contain a statement in a separate paragraph (see
Sec. 1.77(b)(5)) that incorporates by reference the material in the
XML file identifying:
(i) The name of the file;
(ii) The date of creation; and
(iii) The size of the file in bytes; or
(2) If the ``Sequence Listing XML'' required by Sec. 1.831(a) is
submitted in XML file format via the USPTO patent electronic filing
system or on a read-only optical disc (in compliance with Sec.
1.52(e)) for an international application during the international
stage, then an incorporation by reference statement of the material in
the XML file is not required.
Sec. 1.835 Amendment to add or replace a ``Sequence Listing XML'' in
patent applications filed on or after July 1, 2022.
(a) Any amendment to a patent application adding an initial
submission of a ``Sequence Listing XML'' as required by Sec. 1.831(a)
after the application filing date must include:
(1) A ``Sequence Listing XML'' in accordance with Sec. Sec. 1.831
through 1.834, submitted as an XML file:
(i) Via the USPTO patent electronic filing system; or
(ii) On a read-only optical disc, in compliance with Sec. 1.52(e);
(2) A request to amend the specification to include an
incorporation by reference statement of the material in the ``Sequence
Listing XML'' file, identifying the name of the file, the date of
creation, and the size of the file in bytes (see Sec. 1.77(b)(5)(ii)),
except when submitted to the United States International Preliminary
Examining Authority for an international application;
(3) A statement that indicates the basis for the amendment, with
specific references to particular parts of the application as
originally filed (specification, claims, drawings) for all sequence
data in the ``Sequence Listing XML''; and
(4) A statement that the ``Sequence Listing XML'' includes no new
matter.
(b) Any amendment adding to, deleting from, or replacing sequence
information in a ``Sequence Listing XML'' submitted as required by
Sec. 1.831(a) must include:
(1) A replacement ``Sequence Listing XML'' in accordance with the
requirements of Sec. Sec. 1.831 through 1.834 containing the entire
``Sequence Listing XML,'' including any additions, deletions, or
replacements of sequence information, which shall be submitted:
(i) Via the USPTO patent electronic filing system; or
(ii) On a read-only optical disc, in compliance with Sec. 1.52(e),
labeled as ``REPLACEMENT MM/DD/YYYY'' (with the month, day, and year of
creation indicated);
(2) A request to amend the specification to include an
incorporation by reference statement of the material in the replacement
``Sequence Listing XML'' file that identifies the name of the file, the
date of creation, and the size of the file in bytes (see Sec.
1.77(b)(5)(ii)), except when the replacement ``Sequence Listing XML''
is submitted to the United States International Preliminary Examining
Authority for an international application;
(3) A statement that identifies the location of all additions,
deletions, or replacements of sequence information relative to the
replaced ``Sequence Listing XML'';
(4) A statement that indicates the support for the additions,
deletions, or replacements of the sequence information, with specific
references to particular parts of the application as originally filed
(specification, claims, drawings) for all amended sequence data in the
replacement ``Sequence Listing XML''; and
(5) A statement that the replacement ``Sequence Listing XML''
includes no new matter.
(c) The specification of a complete application, filed on the
application filing date, with a ``Sequence Listing XML'' as required
under Sec. 1.831(a), without an incorporation by reference of the
material contained in the ``Sequence Listing XML'' file, must be
amended to include a separate paragraph incorporating by reference the
material contained in the ``Sequence Listing XML'' file, in accordance
with Sec. 1.77(b)(5)(ii), except for international applications.
(d)(1) If any of the requirements of Sec. Sec. 1.831 through 1.834
are not satisfied in an application under 35 U.S.C. 111(a) or in a
national stage application under 35 U.S.C. 371, the applicant will be
notified and given a period of time within which to comply with such
requirements in order to prevent abandonment of the application.
Subject to paragraph (d)(2) of this section, any amendment to add or
replace a ``Sequence Listing XML'' or add an incorporation by reference
of the material contained in the ``Sequence Listing XML'' in response
to a requirement under this paragraph (d)(1) must be submitted in
accordance with the requirements of paragraphs (a) through (c) of this
section.
[[Page 30821]]
(2) Compliance with paragraphs (a) through (c) of this section is
not required for submission of a ``Sequence Listing XML'' that is
solely an English translation of a previously submitted ``Sequence
Listing XML'' that contains non-English values for any language-
dependent free text elements (as per Sec. 1.833(b)(3)). The required
submission will be a translated ``Sequence Listing XML'' in compliance
with Sec. Sec. 1.831 through 1.834. Updated values for attributes in
the root element (Sec. 1.833(b)(2)(iii)) or elements of the general
information part (Sec. 1.833(b)(2)(iv)) are not considered amendments
for purposes of complying with paragraphs (a) through (c) of this
section.
(e) If any of the requirements of Sec. Sec. 1.831 through 1.834
are not satisfied at the time of filing an international application
under the PCT, where the application is to be searched by the United
States International Searching Authority or examined by the United
States International Preliminary Examining Authority, the applicant may
be sent a notice necessitating compliance with the requirements within
a prescribed time period. Under PCT Rule 13ter, the applicant can
provide, in response to such a requirement or otherwise, a sequence
listing that is a ``Sequence Listing XML'' in accordance with Sec.
1.831(a). The ``Sequence Listing XML'' must be accompanied by a
statement that the information recorded does not go beyond the
disclosure in the international application as filed. In response to
such a requirement, the late furnishing fee set forth in Sec.
1.445(a)(5) is also required. If the applicant fails to timely provide
the required ``Sequence Listing XML,'' the United States International
Searching Authority shall search only to the extent that a meaningful
search can be performed without the ``Sequence Listing XML,'' and the
United States International Preliminary Examining Authority shall
examine only to the extent that a meaningful examination can be
performed without the ``Sequence Listing XML.''
(f) Any appropriate amendments to the ``Sequence Listing XML'' in a
patent (e.g., by reason of reissue, reexamination, or certificate of
correction) must comply with the requirements of paragraph (b) of this
section.
Sec. 1.839 Incorporation by reference.
(a) Certain material is incorporated by reference into this subpart
with the approval of the Director of the Federal Register under 5
U.S.C. 552(a) and 1 CFR part 51. All approved incorporation by
reference (IBR) material is available for inspection at the USPTO and
at the National Archives and Records Administration (NARA). Contact the
USPTO's Office of Patent Legal Administration at 571-272-7701. For
information on the availability of this material at NARA, email
[email protected] or go to www.archives.gov/federal-register/cfr/ibr-locations.html. The material may be obtained from the source(s) in
paragraph (b) of this section.
(b) World Intellectual Property Organization (WIPO), 34 chemin des
Colombettes, 1211 Geneva 20 Switzerland, www.wipo.int.
(1) WIPO Standard ST.26. WIPO Handbook on Industrial Property
Information and Documentation, Standard ST.26: Recommended Standard for
the Presentation of Nucleotide and Amino Acid Sequence Listings Using
XML (eXtensible Markup Language) including Annexes I-VII, version 1.5,
approved November 5, 2021; IBR approved for Sec. Sec. 1.831 through
1.834.
(2) [Reserved]
Katherine K. Vidal,
Under Secretary of Commerce for Intellectual Property and Director of
the United States Patent and Trademark Office.
[FR Doc. 2022-10343 Filed 5-19-22; 8:45 am]
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