[Federal Register Volume 86, Number 126 (Tuesday, July 6, 2021)]
[Proposed Rules]
[Pages 35429-35443]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2021-14325]
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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 XML (eXtensible Markup Language) in Patent Applications
To Implement WIPO Standard ST.26; Incorporation by Reference
AGENCY: United States Patent and Trademark Office, Department of
Commerce.
ACTION: Notice of proposed rulemaking.
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SUMMARY: The United States Patent and Trademark Office (USPTO or
Office) is proposing to revise 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 the provisions of Standard ST.26 into the USPTO rules. Other
conforming changes to accommodate for proposed new rules of practice
based on the new standard are also included. These proposed amendments
would apply to international and national applications filed on or
after January 1, 2022. In addition to simplifying the process for
applicants filing in multiple countries, a requirement to submit a
single sequence listing in eXtensible Mark-up Language (XML) format
will result in better preservation, accessibility, and sorting of the
submitted sequence data for the public.
DATES: Comments must be received by September 7, 2021 to ensure
consideration.
ADDRESSES: For reasons of Government efficiency, comments must be
submitted through the Federal eRulemaking Portal at
www.regulations.gov. To submit comments via www.regulations.gov, enter
docket number PTO-P-2021-0006 on the homepage and click ``Search.'' The
site will provide a search results page listing all documents
associated with this docket. Find a reference to this notice and click
on the ``Comment Now!'' icon, complete the required fields, and enter
or attach your comments. Attachments to electronic comments will be
accepted in ADOBE[supreg] portable document format or MICROSOFT
WORD[supreg] format. Because comments will be made available for public
inspection, information that the submitter does not desire to make
public, such as an address or phone number, should not be included in
the comments.
Visit the Federal eRulemaking Portal website (www.regulations.gov)
for additional instructions on providing comments via the portal. If
electronic submission of comments is not feasible due to lack of access
to a computer and/or the internet, please contact the USPTO using the
contact information below for special instructions.
FOR FURTHER INFORMATION CONTACT: Mary C. Till, Senior Legal Advisor,
Office of Patent Legal Administration, Office of the Deputy
Commissioner for Patents, by email at [email protected]; or Ali
Salimi, Senior Legal Advisor, Office of Patent Legal Administration,
Office of the Deputy Commissioner for Patents, by email at
[email protected]. Contact via telephone at 571-272-7704 for special
instructions on submission of comments.
SUPPLEMENTARY INFORMATION:
Table of Contents
I. Background
a. Summary of Changes
b. Introduction
c. Standard ST.26
d. Benefits
e. WIPO Authoring and Validation Tool (WIPO Sequence)
f. Applicability
II. Discussion of Specific Rules
III. Rulemaking Considerations
I. Background
a. Summary of Changes
Standard ST.26 is the new international standard developed by the
World Intellectual Property Organization (WIPO) and member states and
adopted by the same. Under Standard ST.26, patent applications that
contain disclosures of nucleotides and/or amino acid sequence(s) must
present
[[Page 35430]]
the associated biological sequence data in a standardized electronic
format (a ``Sequence Listing XML'') as a separate part of the
specification. Under the proposed rules, in international applications
filed under the Patent Cooperation Treaty (PCT) and in national and
regional applications in Intellectual Property Offices (IPOs) of WIPO
member states, an applicant will have to submit a single
internationally acceptable sequence listing in a language neutral
format using specified International Nucleotide Sequence Database
Collaboration (INSDC) identifiers, such that a single sequence listing
can be prepared for worldwide use.
The proposed rule changes include: (1) Creation of new rules
(Sec. Sec. 1.831 through 1.835) to incorporate by reference Standard
ST.26; (2) use of INSDC sequence data elements to replace numeric
identifiers from the previous standard; (3) modification of rules of
practice to include reference to ``Sequence Listing XML;'' (4)
elimination of a paper or PDF copy of the sequence listing; (5)
elimination of the option to include within a sequence listing
sequences with fewer than 4 amino acids and fewer than 10 nucleotides;
and (6) clarification and simplification of the rules to aid in
understanding of the requirements that they set forth.
b. Introduction
The sequence rules (37 CFR 1.821 through 1.825) provide a
standardized format for description of nucleotide and amino acid
sequence data in patent applications and require the submission of such
sequences in computer readable form (CRF). The current USPTO rules are
based on WIPO Standard ST.25, which became effective in 1998, and use a
flat file structure of numeric identifiers using a limited set of
character codes. A new international standard, ST.26, was agreed upon
by WIPO member states, and would apply to international and national
applications filed on or after January 1, 2022. Applications pending
prior to January 1, 2022, would not have to comply with Standard ST.26.
In an effort to streamline and reduce the procedural requirements
found in the existing rules, and to respond to the needs of our
customers to conform to Standard ST.26, the USPTO is proposing to amend
its rules of practice for submitting biological sequence data
associated with disclosures of nucleotide and amino acid sequences in
patent applications filed on or after January 1, 2022, to comply with
Standard ST.26.
To decrease the burden on applicants who file applications
containing nucleotide and amino acid sequence information
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 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 (hereinafter referred to as a ``Sequence Listing XML''). In
order to obtain public input on the content of Standard ST.26, the
USPTO issued Requests for Comments in 2012 and 2016 (``Request for
Comments on the Recommendation for the Disclosure of Sequence Listings
Using XML (Proposed ST.26).'' (See 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).'' (See 81 FR 74775 (October 27,
2016))). The adopted version of Standard ST.26 takes those comments
into account. To achieve the goals that WIPO and WIPO 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 ST.26 for international and
national applications filed on or after January 1, 2022. Therefore,
upon finalizing the proposed rules, applications filed electronically
in the United States on or after January 1, 2022, would need to conform
to Standard ST.26, which requires submitting sequence listings in XML
format. The USPTO is further proposing that applications that claim
benefit or priority to an earlier application, where the earlier
application contained a sequence listing that complied with the
Standard ST.25 sequence rules, comply with the new rules that
incorporate by reference Standard ST.26. In order to facilitate
compliance, WIPO Sequence, a sequence listing authoring and validating
tool, has been developed by WIPO with input from WIPO member states so
that applicants can use it to prepare and validate their sequence
listings in XML format as discussed infra. The USPTO is proposing to
add to the patent rules (37 CFR part 1) by incorporating by reference
Standard ST.26, and providing conforming amendments to the current
rules.
To ensure that biological sequence data associated with the
disclosures of nucleotides and/or amino acid sequence(s) 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) for inclusion of patent sequence data in the GenBank
searchable database. For NCBI to include all sequence data from the
USPTO, the data must be provided in INSDC format so that 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 provided 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 European Molecular Biology Laboratory, European Bioinformatics
Institute (EMBL-EBI). WIPO has been working with the WIPO member states
to create, adopt, and implement Standard ST.26 for sequence listing
submissions in XML file format having the INSDC data elements to
address the data loss. Standard ST.26 aims to enhance the accuracy and
quality of biological sequence data that is publicly disseminated. In
adopting and implementing Standard ST.26, more complete biological
sequence data from patents and patent applications will be included in
GenBank and thus be accessible by the public. The change from ASCII
format to XML format will result in sequence data having computer tags
that facilitate sorting and retrieving, and permit ease of access to
the data. Additionally, NCBI is planning to stop accepting data in
Standard ST.25 format for inclusion in GenBank in about 3-5 years after
January 1, 2022 (the Standard ST.26 transition date).
c. Standard ST.26
The WIPO ``Handbook on Industrial Property Information and
Documentation'' sets forth standards for the presentation of data in
many contexts. Standard ST.26 is titled ``Recommended Standard for the
Presentation of Nucleotide and Amino Acid Sequence Listings Using XML
(eXtensible Markup Language).'' Adoption of the current version,
version 1.4, by the CWS, occurred in December of 2020 and reaffirms
that January 1, 2022, is expected to be the implementation date for all
WIPO member states. The proposed USPTO rules incorporate by reference
Standard ST.26.
[[Page 35431]]
The adopted version of Standard ST.26 is composed of eight
documents, namely, the main body of the Standard, a first annex setting
forth the controlled vocabulary for use with the main body, a second
annex setting forth the Document Type Definition (DTD) for the
Standard, a third annex containing a sequence listing specimen, a
fourth annex setting forth the character subset from the Unicode Basic
Latin Code Table, a fifth annex setting forth additional data exchange
requirements for IPOs, a sixth annex containing a guidance document,
and a seventh annex setting forth recommendations for the
transformation of a sequence listing from Standard ST.25 format to
Standard ST.26 format including avoiding adding or deleting subject
matter. These materials can be found at http://www.wipo.int/export/sites/www/standards/en/pdf/03-26-01.pdf. The main body of Standard
ST.26 defines the disclosures of nucleotide and amino acid sequences in
patent applications that must be presented in a sequence listing in XML
format in the manner specified in the Standard. Specifically, as
detailed in paragraph eight of the main body, a sequence listing must
not include, as a sequence assigned its own sequence identification
number, any sequences having fewer than ten specifically defined
nucleotides, or fewer than four specifically defined amino acids. The
main body establishes the requirements for representation of nucleotide
and amino acid sequences and the requirements for the XML file format
for a sequence listing. The first annex 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, the first annex provides
defined feature keys and qualifiers used for nucleotide and amino acid
sequences in the XML file for a sequence listing. This first annex
specifically identifies qualifiers with language-dependent ``free
text'' values that may require translation for national and regional
procedures. The second annex provides the DTD setting forth the
technical specifications to which a submitted Sequence Listing XML must
conform. The third annex provides a specimen of a Standard ST.26
compliant sequence listing 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
for a ``Sequence Listing XML.'' 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, is provided to ensure 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 comment in 2012 and 2016, mentioned above. The
guidance document illustrates the requirements of selected paragraphs
found in the main body of 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 within a Standard ST.26 compliant sequence listing
in XML format. Annex VII addresses the potential consequence of these
requirements when transforming a compliant Standard ST.25 sequence
listing to a Standard ST.26 sequence listing, and provides detailed
guidance on avoiding added or deleted subject matter due to the
additional requirements of Standard ST.26.
d. Benefits
Transitioning from rules based on Standard ST.25 (i.e., the current
basis for the USPTO rules for ``Sequence Listings'') to rules based on
Standard ST.26 will be beneficial to both patent applicants filing
sequence listings and IPOs receiving applications containing
disclosures of nucleotide and amino acid sequences. Standard ST.26
provides clear requirements as to 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 Standard ST.26 contains a guidance document that
illustrates the requirements for inclusion and representation of
biological sequence data, patent applicants will have a clearer
understanding of the requirements for presentation of biological
sequence data in a compliant sequence listing under Standard ST.26.
Additionally, since Standard ST.26 only allows XML format, the
potential for differences under the current rules between a sequence
listing filed in paper/PDF format and the required electronic CRF will
be eliminated. As a further benefit, 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 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 WIPO member
states. Under Standard ST.25, IPOs have interpreted and enforced rules
differently due to the imprecise language in the previous Standard.
This has resulted in the frustrating situation where applicants
generate sequence listings that may be accepted in one IPO but not
another.
Standard ST.26 was drafted to precisely define what must and must
not be included in a sequence listing, and how sequences must be
represented in a sequence listing. The ``Guidance document with
illustrated examples'' in Annex VI of Standard ST.26 illustrates the
application of the rules to real-world sequence disclosure examples,
eliminating the possibility of misinterpretation by IPOs or applicants.
Due to the improved data structure of XML, transitioning from the
current USPTO rules based on Standard ST.25 to rules based on Standard
ST.26 will have the effect of increasing the quality of examination of
patent applications containing biological sequence data since a more
comprehensive search will be possible. Sequence listings submitted in
accordance with 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 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. Standard ST.26
standardizes sequence variant presentation, annotation of modified and
unusual residues, feature location descriptors, use of feature keys and
qualifiers, organism names, and presentation of coding regions.
Incorporation by reference of Standard ST.26 into USPTO rules has the
effect of promoting data exchange between USPTO and NCBI due to 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 for
biotechnology stakeholders that relate to nucleotide and amino acid
sequences.
[[Page 35432]]
The USPTO recommends requiring compliance with Standard ST.26 for
an application filed on or after January 1, 2022, because it will
reduce the complexity and cost of long-term maintenance of IT systems
for accepting sequence listings in multiple formats, provide a clear
implementation date, and will facilitate 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. As noted herein, WIPO has created a tool to assist
applicants with translation of existing sequences to the new standard.
e. WIPO Authoring and Validation Tool (WIPO Sequence)
To comply with rules that are based on Standard ST.26, patent
applicants will be able to use ``WIPO Sequence,'' a freely-available
desktop application developed by WIPO and adopted by WIPO member
states, to generate a Standard ST.26 compliant sequence listing. 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
Standard ST.26. Such a sequence listing will be accepted by all IPOs of
WIPO member states. Thus, the burden of generating a sequence listing
which is acceptable across all WIPO member states will be significantly
decreased for patent applicants under Standard ST.26. This tool will be
downloadable, free of charge, from the WIPO website. Currently, a beta
version of WIPO Sequence is accessible at https://www.wipo.int/standards/en/sequence/index.html. This beta version will allow the
public to familiarize themselves with the tool and its dual
functionalities.
WIPO Sequence will allow a user to create and save 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 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 Standard ST.26 projects, 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 within WIPO
Sequence for ease of access. To facilitate review of data entered into
a project, WIPO Sequence can generate a ``human-readable'' version 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
that are contained 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 Standard ST.26 format because certain data elements
required for a Standard ST.26 compliant sequence listing 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 USPTO (in Annex VI and Annex VII of
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 in comment to 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.
In order 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 ``Sequence Listing XMLs'' (Sec. Sec. 1.831
through 1.835) and accepted since the WIPO Sequence Validator that
USPTO will use is based on Standard ST.26, which is incorporated by
reference into the USPTO proposed rules of practice.
e. Applicability
In accordance with these proposed rules of practice, an application
that has a filing date on or after January 1, 2022, would be required
to contain a sequence listing in accordance with proposed Sec. Sec.
1.831 through 1.835, which incorporate by reference Standard ST.26.
This includes applications that claim priority to applications with
filing dates before January 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),
section 120 (claiming the benefit as a continuation and/or
continuation-in-part), section 121 (claiming the benefit as a
divisional), section 365 (claiming the benefit as a continuation or
continuation in part to a PCT application), or section 119(a)-(d)
(claiming the benefit 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, the applicant
would be required to convert that sequence listing to Standard ST.26
format for inclusion in the new application filed on or after January
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 filed under 35 U.S.C. 371, compliance with Standard ST.26
is 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. The proposed rules would also
be applicable to applications for reissue without
[[Page 35433]]
regard to the filing date of the originally granted patent for which
reissue is sought. That is, any reissue application filed on or after
January 1, 2022, where the disclosure or claims contain nucleotide and
amino acid sequences would be required to comply with proposed
Sec. Sec. 1.831 through 1.835.
Relying on the actual filing date of an application to determine
whether a sequence listing must conform to Sec. Sec. 1.821 through
1.825 (rules based on Standard ST.25) or Sec. Sec. 1.831 through 1.835
(rules based on Standard ST.26) will simplify the application of the
sequence rules, both for the USPTO and the applicant.
II. Discussion of Specific Rules
Section 1.52: Paragraph (e)(1)(ii) was proposed to be amended in
another rulemaking that published at 86 FR 28301 (May 26, 2021). This
proposed rule would further amend that paragraph 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)(iv) is proposed to be 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) was proposed to be amended in another rulemaking
that published at 86 FR 28301 (May 26, 2021). This proposed rule would
further amend that paragraph to require that any amendment to the
information on a read-only optical disc submitted in relation to a
``Sequence Listing XML'' be in accordance with Sec. 1.835(b).
Section 1.52(f)(1) was proposed to be amended in another rulemaking
that published at 86 FR 28301 (May 26, 2021). This proposed rule would
further amend that paragraph to indicate 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 ``any
sequence listing.''
Section 1.52(f)(1)(i) was proposed to be added in another
rulemaking that published at 86 FR 28301 (May 26, 2021). This proposed
rule would further amend that paragraph to reference any ``Sequence
Listing XML'' in compliance with Sec. 1.831(a).
Section 1.52(f)(2) was proposed to be amended in another rulemaking
that published at 86 FR 28301 (May 26, 2021). This proposed rule would
further amend that paragraph 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 electronic medium from the application size fee
determination. A ``Sequence Listing XML'' is considered ``any sequence
listing.''
Section 1.52(f)(2)(i) was proposed to be added in another
rulemaking that published at 86 FR 28301 (May 26, 2021). This proposed
rule would further amend that paragraph to reference any ``Sequence
Listing XML'' in compliance with Sec. 1.831(a).
Section 1.52(f)(3) was proposed to be added in another rulemaking
that published at 86 FR 28301 (May 26, 2021). This proposed rule would
further amend that paragraph to subject any ``Sequence Listing XML'' of
300MB-800MB to the surcharge set forth in Sec. 1.21(o)(1) and any
``Sequence Listing XML'' over 800MB to the surcharge set forth in Sec.
1.21(o)(2).
Section 1.53: Section 1.53(c)(4) is proposed to be 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 January 1, 2022, must be a ``Sequence Listing XML''
in compliance with Sec. Sec. 1.831 through 1.834. This proposed change
is not anticipated to cover applications filed before January 1, 2022.
Section 1.77: Section 1.77(b)(5) was proposed to be amended in
another rulemaking that published at 86 FR 28301 (May 26, 2021). This
proposed rule would further amend that paragraph by reorganizing under
Sec. 1.77(b)(5)(i) the provisions for an incorporation by reference
statement for ASCII plain text tiles 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) would contain provisions for
an incorporation by reference statement for a ``Sequence Listing XML''
submitted via a USPTO patent electronic filing system or on one or more
read-only optical discs. There would be no Sec. 1.77(b)(5)(iii).
Section 1.121: Section 1.121(b) was proposed to be amended in
another rulemaking that published at 86 FR 28301 (May 26, 2021). This
proposed rule would further amend that paragraph to add an exception to
amendment practice for ``Sequence Listing XML''s (Sec. 1.835).
Section 1.121(b)(6) was proposed to be added in another rulemaking
that published at 86 FR 28301 (May 26, 2021). This proposed rule would
further amend that paragraph 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) was proposed to be
amended in another rulemaking that published at 86 FR 28301 (May 26,
2021). This proposed rule would further amend that heading to include `
``Sequence Listing XML' (Sec. 1.831(a)).''
Section 1.173(b)(1)(i) was proposed to be added in another
rulemaking that published at 86 FR 28301 (May 26, 2021). This proposed
rule would further amend that paragraph to add an exception to reissue
amendment practice for a ` ``Sequence Listing XML' (Sec. 1.831(a)).''
Section 1.173(b)(1)(ii) was proposed to be added in another
rulemaking that published at 86 FR 28301 (May 26, 2021). This proposed
rule would further amend that paragraph to provide that changes to a
``Sequence Listing XML'' must be made in accordance Sec. 1.835.
Section 1.173(d) was proposed to be amended in another rulemaking
that published at 86 FR 28301 (May 26, 2021). This proposed rule would
further amend that paragraph to also exclude a ``Sequence Listing XML''
from the manner of making amendments in a reissue application.
Section 1.211: Section 1.211(c) is proposed to be amended to add a
``Sequence Listing'' in compliance with Sec. Sec. 1.821 through 1.825
(if applicable) for an application filed before January 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 January 1,
2022, to the currently listed items that may delay application
publication if not present.
Section 1.495: Section 1.495(c)(5) is proposed to be amended to
delineate between translations needed for a ``Sequence Listing'' in
international applications entering the national stage in the United
States having an international filing date before January 1, 2022, and
a ``Sequence Listing'' in XML format for international applications
entering the national stage in the United States having an
international filing date on or after January 1, 2022. Specifically,
the
[[Page 35434]]
proposed amendment indicates that a ``Sequence Listing'' need not be
translated for national stage entry if the ``Sequence Listing''
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
January 1, 2022. However, the proposed amendment indicates that a
``Sequence Listing'' in XML format must be translated for national
stage entry if a ``Sequence Listing'' in XML format was submitted in an
international application with non-English language values for the
invention title and/or any language-dependent free text qualifiers and
has an international filing date on or after January 1, 2022.
Section 1.530: The heading of Sec. 1.530(d)(1) was proposed to be
amended in another rulemaking that published at 86 FR 28301 (May 26,
2021). This proposed rule would further amend that heading to include `
``Sequence Listing XML' (Sec. 1.831(a)).''
Section 1.530(d)(1)(i) was proposed to be added in another
rulemaking that published at 86 FR 28301 (May 26, 2021). This proposed
rule would further amend that paragraph to add an exception to
reexamination amendment practice for a ` ``Sequence Listing XML' (Sec.
1.831(a)).''
Section 1.530(d)(1)(ii) was proposed to be added in another
rulemaking that published at 86 FR 28301 (May 26, 2021). This proposed
rule would further amend that paragraph 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 proposed to be amended to add a
``Sequence Listing XML'' in compliance with Sec. Sec. 1.831 through
1.835 (if applicable) to the list of items that are 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 proposes to add a ``Sequence Listing
XML'' in compliance 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 proposed to be 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 for which an
application is considered to be in compliance, 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 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.
Section 1.831: Section 1.831 is proposed to be added to require
that patent applications having disclosures of nucleotide and amino
acid sequences, as those terms are defined in the rule, must contain,
as a separate part of the disclosure, a ``Sequence Listing XML'' for
patent applications having a filing date on or after January 1, 2022.
Section 1.831(a) is proposed to be added to specify that the
``Sequence Listing XML'' uses 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 proposed to be added to define the
nucleotide and amino acid sequences that are encompassed by the rule
for which a ``Sequence Listing XML'' is needed. Specifically,
nucleotide and/or amino acid sequences as used in these proposed rules
encompass: An unbranched sequence or linear region of a branched
sequence containing four 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 proposed to be added to state that, 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. 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 specification or claims where it is clear that a sequence from the
``Sequence Listing XML'' is shown in the specification or claims. In
identifying the sequence in the description or claims, the numeric
sequence identifier from the ``Sequence Listing XML'' must be
identifying the same sequence.
Section 1.831(d) is proposed to be added to define the expression
``enumeration of its residues,'' consistent with the definition in
Paragraph 3(c) of WIPO Standard ST.26 itself (which is incorporated by
reference herein).
Section 1.831(e) is proposed to be added to define the expression
``specifically defined,'' consistent with the definition in Paragraph
3(m) of WIPO Standard ST.26 (2020).
Section 1.831(f) is proposed to be added to define the expression
``amino acid,'' consistent with the definition in Paragraph 3(a) of
WIPO Standard ST.26 (2020).
Section 1.831(g) is proposed to be added to define the expression
``modified amino acid,'' consistent with the definition in Paragraph
3(g) of WIPO Standard ST.26 (2020).
Section 1.831(h) is proposed to be added to define the expression
``nucleotide,'' consistent with Paragraphs 3(h) and 3(i) of WIPO
Standard ST.26 (2020).
Section 1.831(i) is proposed to be added to define the expression
``modified nucleotide,'' consistent with Paragraph 3(h) of WIPO
Standard ST.26 (2020).
Section 1.832: Section 1.832 is proposed to be added to provide the
manner in which a nucleotide and/or amino acid sequence is presented in
the ``Sequence Listing XML'' part of a patent application having a
filing date on or after January 1, 2022.
Section 1.832(a) is proposed to be added to define the requirements
for representation of sequences in a ``Sequence Listing XML'' part of
the application. Specifically, each nucleotide and/or amino acid
sequence presented in the ``Sequence Listing XML'' must be assigned a
separate sequence identifier, and the sequence identifiers must begin
with the number 1, and increase sequentially by integers as defined in
Paragraph 10 of WIPO Standard ST.26 (2020).
Section 1.832(b)(1) through (4) are proposed to be added to define
the requirements for 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 (2020). All nucleotides, including nucleotide analogs,
modified nucleotides, ``unknown'' nucleotides in a nucleotide sequence
must be represented and described using symbols in the manner described
in Paragraphs 13-19 and 21 of WIPO
[[Page 35435]]
Standard ST.26 (2020). 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 (2020).
Section 1.832(c)(1) through (4) are proposed to be added to define
the requirements for 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 24-25 of WIPO
Standard ST.26 (2020). All amino acids, including modified amino acids
and ``unknown'' amino acids, in an amino acid sequence must be
represented and described using symbols in the manner described in
Paragraphs 24-30 and 32 of WIPO Standard ST.26 (2020). For a region
containing a known number of contiguous ``X'' residues for which the
same description applies, the entire region may be jointly described as
provided in Paragraph 34 of WIPO Standard ST.26 (2020).
Section 1.832(d) is proposed to be added to define the manner in
which a single continuous sequence, derived from one or more non-
contiguous segments of a larger sequence, or from segments of different
sequences, must be represented, as described in Paragraph 35 of WIPO
Standard ST.26 (2020).
Section 1.832(e) is proposed to be 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, as described in Paragraph 36 of WIPO Standard ST.26
(2020).
Section 1.832(f) is proposed to be added to define the manner in
which 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, as
described in Paragraph 37 of WIPO Standard ST.26 (2020).
Section 1.833: Section 1.833 is proposed to be added to describe
the requirements for a ``Sequence Listing XML,'' which is required by
Sec. 1.831(a) for patent applications with a filing date on or after
January 1, 2022, in order to comply with WIPO Standard ST.26 (2020).
Section 1.833(a) is proposed to be 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(b)(1) is proposed to be added to require that the
``Sequence Listing XML'' must be valid according to the DTD as
presented in Annex II of WIPO Standard ST.26 (2020).
Section 1.833(b)(2) is proposed to be added to require that a
``Sequence Listing XML'' must comply with the list of items enumerated
in (i)-(v) which are found in WIPO Standard ST.26 (2020).
Section 1.833(b)(2)(i) is proposed to be added to require that the
``Sequence Listing XML'' contain an XML declaration as defined in WIPO
Standard ST.26 (2020), Paragraph 39.
Section 1.833(b)(2)(ii) is proposed to be added to require that the
``Sequence Listing XML'' contain a document type declaration as defined
in WIPO Standard ST.26 (2020), Paragraph 39.
Section 1.833(b)(2)(iii) is proposed to be added to require that
the ``Sequence Listing XML'' contain a root element as defined in WIPO
Standard ST.26 (2020), Paragraph 43.
Section 1.833(b)(2)(iv) is proposed to be added to require that the
``Sequence Listing XML'' contain a general information part that
complies with WIPO Standard ST.26 (2020), Paragraphs 45, 47 and 48, as
applicable.
Section 1.833(b)(2)(v) is proposed to be added to require that the
``Sequence Listing XML'' contain a sequence data part that complies
with WIPO Standard ST.26 (2020), Paragraphs 50-55, 57-58, 60-69, 71-78,
80-87, 89-98 and 100, as applicable.
Section 1.833(b)(3) is proposed to be added to require that the
``Sequence Listing XML'' contains at least one InventionTitle element,
as set forth in WIPO Standard ST.26 at Paragraphs 45 and 48, in the
English language since English is required under Sec. 1.52(b)(1)(ii).
Section 1.833(b)(4) is proposed to be added to require that an
INSDQualifier_value element includes a value for that element in the
English language 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 WIPO Standard ST.26
(2020), Paragraphs 76 and 85-88.
Section 1.834: Section 1.834 is proposed to be 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 January 1, 2022.
Section 1.834(a) is proposed to be 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) Have the following compatibilities: (i) Computer
compatibility: PC or Mac[supreg]; and (ii) operating system
compatibility (e.g., 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 (2020); 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 proposed to be 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 1.835: Section 1.835 is proposed to be added to provide the
requirements for submission of an amendment to add or replace a
``Sequence Listing XML'' for applications filed on or after January 1,
2022.
Section 1.835(a) is proposed to be 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) an instruction 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
[[Page 35436]]
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 proposed to be 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 proposed to be 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 proposed to be added to provide that when
any of the requirements of Sec. Sec. 1.831 through 1.834 is 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. The
proposed rule indicates that subject to Sec. 1.835(d)(2), any
amendment to add or replace a ``Sequence Listing XML'' in reply 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 proposed to be added to explicitly provide
that compliance with Sec. 1.835(a) through (c) 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 the invention title (as per Sec.
1.833(b)(3)) and/or any language-dependent free text elements (as per
Sec. 1.833(b)(4)). 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 111(a) and for those entering the national
stage, respectively, this proposed 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 the
invention title and/or any language-dependent free text elements, and
the translation does not include deletions, additions 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).
Section 1.835(e) is proposed to be 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, applicant can provide, in reply to such a
requirement or otherwise, a sequence listing which 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. It must also be accompanied by the late furnishing fee set forth
in Sec. 1.445(a)(5). 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 proposed to be 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 proposed to be added to provide the
location of WIPO Standard ST.26 (2020) that is being incorporated by
reference.
III. Rulemaking Considerations
A. Administrative Procedure Act: The changes proposed 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) (rules governing an application process are procedural
under the Administrative Procedure Act); Inova Alexandria Hosp. v.
Shalala, 244 F.3d 342, 350 (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) (rule that
clarifies interpretation of a statute is interpretive).
Accordingly, prior notice and opportunity for public comment for
the changes proposed in this rulemaking are 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 has chosen to seek public comment
before
[[Page 35437]]
implementing the rule to benefit from the public's input.
B. Regulatory Flexibility Act: Under the Regulatory Flexibility Act
(5 U.S.C. 601 et seq.), whenever an agency is required by 5 U.S.C. 553
(or any other law) to publish a notice of proposed rulemaking (NPRM),
the agency must prepare and make available for public comment an
Initial Regulatory Flexibility Analysis, unless the agency certifies
under 5 U.S.C. 605(b) that the proposed rule, if implemented, will not
have a significant economic impact on a substantial number of small
entities. 5 U.S.C. 603, 605.
For the reasons set forth herein, 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 proposes to amend the rules of practice to require
submission of biological sequence data in eXtensible Markup Language
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)''
as disclosed in the WIPO Handbook on Industrial Property Information
and Documentation.
This rulemaking would make more technical data associated with
biotechnology inventions available to the public because the new rules
of practice based on WIPO Standard ST.26 (2020) provide for enhanced
biological sequence data related to disclosures of nucleotides and
amino acids 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, for example, standardization of
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 or
confused with 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. This rulemaking's proposed changes are largely
procedural in nature, and do not impose any additional requirements or
fees on applicants. For the foregoing reasons, the changes proposed in
this NPRM 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 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 effect 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.), prior to issuing any final rule, 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
[[Page 35438]]
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 proposed 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 proposed rulemaking will
be submitted to OMB for approval prior to this rule becoming effective.
Modifications include the removal of the Sequence Listing in
Application (paper), which will result in a reduction in burden
associated with this information collection. The USPTO estimates that
this information collection's annual burden will decrease 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 proposed rule.
The changes discussed in this proposed 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 proposes to further
amend 37 CFR part 1 (as proposed to be amended at 86 FR 28301 (May 26,
2021)) as follows:
PART 1--RULES OF PRACTICE IN PATENT CASES
0
1. The authority citation for 37 CFR 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 paragraph (e)(1)(ii);
0
b. Removing the period at the end of paragraph (e)(3)(iii) and adding
``; and'' in its place;
0
c. Adding paragraph (e)(3)(iv); and
0
d. 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. 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) * * *
(iv) 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.
* * * * *
(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 Computer Readable Form (CRF) of a ``Sequence Listing,''
and Sec. 1.835(b) for a ``Sequence Listing XML.''
* * * * *
(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 of 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) 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.
* * * * *
[[Page 35439]]
(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 January 1, 2022, any
submission of biological sequence data must be 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
on the:
(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) eXtensible Markup Language (XML) file of the Sequence Listing
(``Sequence Listing XML''), submitted via an 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 (Sec. 1.831(a)).
* * * * *
0
5. Section 1.121 is amended by revising paragraphs (b) introductory
text and (b)(6) 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'' or CRF
(Sec. 1.825), or ``Sequence Listing XML''s (Sec. 1.835), must be made
by adding, deleting, or replacing a paragraph, by replacing a section,
or by a substitute specification, in the manner specified in this
section.
* * * * *
(6) ``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,'' and 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,'' a ``Computer Program Listing
Appendix,'' a ``Sequence Listing,'' or a ``Sequence Listing XML'', 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;
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 January 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 January 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) Translations of a ``Sequence Listing:'' For international
applications having an international filing date before January 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 January 1, 2022, for purposes of
paragraph (c)(1)(i) of this section, an English translation is required
for any ``Sequence Listing'' in XML format containing non-English
language values for the invention title/and or 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
[[Page 35440]]
``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,'' and 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 the application 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 the application 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), the 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, or
sequence listing 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 January
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 January 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 January 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 January 1, 2022.
1.835 Amendment to add or replace a ``Sequence Listing XML'' in
patent applications filed on or after January 1, 2022.
1.839 Incorporation by reference.
* * * * *
Sec. 1.831 Requirements for patent applications filed on or after
January 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 (eXtensible Markup Language)
format (a ``Sequence Listing XML''). Disclosed nucleotide or amino acid
sequences that do not meet the definition of paragraph (b) of this
section must not be included in the ``Sequence Listing XML.'' The
``Sequence Listing XML'' contains the sequence information of the
nucleotides and/or amino acids disclosed in the patent application
using the symbols and format in accordance with the requirements of
Sec. Sec. 1.832 through 1.834.
(b) Nucleotide and/or amino acid sequences as used in Sec. Sec.
1.831 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.
(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 WIPO Standard ST.26 (2020)
(incorporated by reference, see Sec. 1.839), paragraph 3(c)(i) or
(ii).
(e) ``Specifically defined'' means any amino acid or nucleotide as
defined in WIPO Standard ST.26 (2020), paragraph 3(m).
(f) ``Amino acid'' includes any D- or L-amino acid or modified
amino acid as defined in WIPO Standard ST.26 (2020), paragraph 3(a).
(g) ``Modified amino acid'' includes any amino acid as described in
WIPO Standard ST.26 (2020), paragraph 3(g).
(h) ``Nucleotide'' includes any nucleotide, nucleotide analog or
modified nucleotide as defined in WIPO Standard ST.26 (2020),
paragraphs 3(h) and 3(i).
(i) ``Modified nucleotide'' includes any nucleotide as described in
WIPO Standard ST.26 (2020), paragraph 3(h).
[[Page 35441]]
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 January 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 WIPO Standard ST.26 (2020) (incorporated by reference, see
Sec. 1.839), paragraph 10.
(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 WIPO Standard ST.26 (2020), paragraphs 11-12.
(2) All nucleotides, including nucleotide analogs, modified
nucleotides, and ``unknown'' nucleotides, within a nucleotide sequence
must be represented using the symbols set forth in WIPO Standard ST.26
(2020), paragraphs 13-16, 19 and 21.
(3) Modified nucleotides within a nucleotide sequence must be
described in the manner discussed in WIPO Standard ST.26 (2020),
paragraphs 17-18, and 19.
(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 WIPO Standard ST.26
(2020), paragraph 22.
(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 WIPO Standard ST.26 (2020), paragraphs 24-
25.
(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 WIPO Standard ST.26 (2020), paragraphs 26-29
and 32.
(3) Modified amino acid within an amino acid sequence must be
described in the manner discussed in WIPO Standard ST.26 (2020),
paragraphs 29 and 30.
(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 WIPO Standard ST.26 (2020), paragraph 34.
(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 from segments of different sequences
must be listed in a sequence listing in the manner described in WIPO
Standard ST.26 (2020), paragraph 35.
(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 a
sequence listing in the manner described in WIPO Standard ST.26 (2020),
paragraph 36.
(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 a sequence
listing in the manner described in WIPO Standard ST.26 (2020),
paragraph 37.
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 January 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 WIPO Standard ST.26 (2020)
(incorporated by reference, see Sec. 1.839), paragraphs 40 and 41 and
Annex IV thereof.
(b) The ``Sequence Listing XML'' as required by Sec. 1.833(a)
must:
(1) Be valid according to the Document Type Definition (DTD) as
presented in Annex II of WIPO Standard ST.26 (2020).
(2) Comply with the requirements of WIPO Standard ST.26 (2020) to
include:
(i) An XML declaration as defined in WIPO Standard ST.26 (2020),
paragraph 39;
(ii) A document type (DOCTYPE) declaration as defined in WIPO
Standard ST.26 (2020), paragraph 39;
(iii) A root element as defined in WIPO Standard ST.26 (2020),
paragraph 43;
(iv) A general information part that complies with the requirements
of WIPO Standard ST.26 (2020), paragraphs 45, 47 and 48, as applicable;
and
(v) A sequence data part that complies with the requirements of
WIPO Standard ST.26 (2020), paragraphs 50-55, 57-58, 60-69, 71-78, 80-
87, 89-98 and 100, as applicable.
(3) Include one InventionTitle element in the English language, in
the format required by WIPO Standard ST.26 (2020), paragraphs 45 and
48, and as required by Sec. 1.52(b)(1)(ii).
(4) Include an INSDQualifier_value element with a value in the
English language for any language-dependent free text qualifier as
defined by WIPO Standard ST.26 (2020), paragraphs 76 and 85-88, 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 January 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 WIPO Standard ST.26 (2020) (incorporated by reference,
see Sec. 1.839), paragraph 40.
(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; 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
[[Page 35442]]
optical disc size, and labeled in compliance with Sec. 1.52(e)(5)(vi).
Sec. 1.835 Amendment to add or replace a ``Sequence Listing XML'' in
patent applications filed on or after January 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, and 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 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 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.
(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'' in reply to a requirement under this
paragraph (d)(1) must be submitted in accordance with the requirements
of paragraphs (a) through (c) of this section.
(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 the invention title
(as per Sec. 1.833(b)(3)) and/or any language-dependent free text
elements (as per Sec. 1.833(b)(4)). 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 applicant can provide,
in reply to such a requirement or otherwise, a sequence listing which
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. It must also be accompanied by the
late furnishing fee set forth in Sec. 1.445(a)(5). 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 approval of the Director of the Federal
Register under 5 U.S.C. 552(a) and 1 CFR part 51. All approved material
is available for inspection at The United States Patent and Trademark
Office, Office of Patent Legal Administration, 571-272-7701, and from
the sources listed elsewhere in this section. It is also available for
inspection at the National Archives and Records Administration (NARA).
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.
(b) World Intellectual Property Organization (WIPO); 34 chemin des
Colombettes; 1211 Geneva 20 Switzerland, www.wipo.int.
(1) WIPO Standard ST.26 (2020). WIPO Handbook on Industrial
Property Information and Documentation, Standard ST.26: Recommended
[[Page 35443]]
Standard for the Presentation of Nucleotide and Amino Acid Sequence
Listings Using XML (eXtensible Markup Language) (2020), including
Annexes I-VII (www.wipo.int/export/sites/www/standards/en/pdf/03-26-01.pdf); IBR approved for Sec. Sec. 1.831 through 1.834.
(2) [Reserved]
Andrew Hirshfeld,
Commissioner for Patents, Performing the Functions and Duties of the
Under Secretary of Commerce for Intellectual Property and Director of
the United States Patent and Trademark Office.
[FR Doc. 2021-14325 Filed 7-2-21; 8:45 am]
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