2418 WIPO Sequence Tool [R-01.2024]
[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b).]
To comply with rules based on WIPO Standard ST.26 (i.e., 37 CFR 1.831 - 1.835), patent applicants can generate a compliant “Sequence Listing XML” using WIPO Sequence, a desktop application developed by WIPO and adopted by WIPO member states, including the US. WIPO Sequence has two functions: An authoring function and a validation function. Patent applicants are able to author and validate their “Sequence Listing XML” using WIPO Sequence to comply with the requirements of WIPO Standard ST.26. A “Sequence Listing XML” that passes validation by WIPO Sequence will be accepted by all the IPOs of the WIPO member states, although translation may be needed. Thus, the burden of generating a WIPO Standard ST.26 compliant sequence listing in XML file format that is acceptable across all WIPO member states will be significantly decreased for patent applicants under WIPO Standard ST.26. This tool is downloadable, free of charge, from the WIPO website. The current version of WIPO Sequence is accessible at www.wipo.int/standards/en/sequence/index.html.
The first step to generate a new sequence listing using WIPO Sequence is to create a project. The user saves (authors) patent application data and biological sequence data in the project, validates the project to ensure all required sequence-associated information is present, and generates a “Sequence Listing XML” in compliance with 37 CFR 1.831 - 1.834 (complying with WIPO Standard ST.26 in XML format). Information can be entered into a project manually, or data can be imported from a source file in one of a number of file types. WIPO Sequence can import data from other WIPO Standard ST.26 projects, WIPO Standard ST.26 XML sequence listings, WIPO Standard ST.25 sequence listing text files, raw data files, multi-sequence format files, and FASTA format files. The entry of sequence-associated data, such as feature keys, qualifiers, and organism names, are facilitated by their selection from drop-down lists, simplifying the creation of a sequence listing. Applicant and inventor names, as well as custom organism names, can be stored in WIPO Sequence for easy access from other projects. To facilitate the review of data entered into a project, WIPO Sequence can generate a “human-readable” version (a text version of the sequence data) of the “Sequence Listing XML.” This human readable version must not be submitted in a patent application.
WIPO Sequence includes an integrated validation function that will alert users to most errors in a project (i.e., “Sequence Listing XML” 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 XML.” While the validation function will alert a user to most errors in a project or “Sequence Listing XML,” 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 XML.” The WIPO Sequence validation function can also be used to validate a “Sequence Listing XML” that was previously generated. As for validation of a project, the validation of a “Sequence Listing XML” generates a report that clearly lists every detected error, the location of the error, and the detected value of the error in the “Sequence Listing XML.” It is highly recommended that a “Sequence Listing XML” produced by WIPO Sequence be validated following its generation.
To ensure that IPOs can validate applicant-submitted sequence listings generated with WIPO Sequence, WIPO developed a Standard ST.26 sequence listing validation tool, WIPO Sequence Validator. WIPO Sequence Validator is for use by IPOs to verify that filed sequence listings comply with WIPO Standard ST.26 . WIPO Sequence Validator is synchronized with the validation function in the WIPO Sequence tool such that WIPO Sequence Validator applies the same validation rules as WIPO Sequence. The USPTO has integrated WIPO Sequence Validator into its internal IT systems (i.e., CRFValidator). Therefore, filers will have a greater level of confidence that a “Sequence Listing XML” validated by WIPO Sequence will comply with the USPTO rules for a “Sequence Listing XML” (37 CFR 1.831 through 1.835) and be accepted.
A “Sequence Listing” in WIPO Standard ST.25 format cannot automatically be converted into WIPO Standard ST.26 format primarily because certain data elements required for a “Sequence Listing XML” compliant with WIPO Standard ST.26 are not present in WIPO Standard ST.25 sequence listing. Therefore, conversion of a “Sequence Listing” in WIPO Standard ST.25 format to WIPO Standard ST.26 format necessarily requires additional input from the applicant. WIPO Sequence, supplemented by significant guidance in Annex VI and Annex VII of WIPO Standard ST.26, will help applicants to accomplish this task without added or deleted subject matter. Users can import a WIPO Standard ST.25 “Sequence Listing” into a project, and WIPO Sequence automatically performs many of the necessary conversions. An Import Report is generated that alerts the user to all data conversions and lists all sequence entries that require additional input. In response to concerns raised regarding the USPTO’s requests for comments in 2012 and 2016, the USPTO, in conjunction with WIPO, developed Annex VII to provide detailed guidance to help applicants avoid added or deleted subject matter when converting a “Sequence Listing” in WIPO Standard ST.25 format into a WIPO Standard ST.26 “Sequence Listing XML” format.
A sample sequence listing (XML file) specimen can be found in WIPO Standard ST.26, Annex III and at www.wipo.int/standards/en/xml_material/st26/ st26-annex-iii-sequence-listing-specimen.xml.
