Biological Sequence Listing Using XML in Patent Applications: Implementation Plan And Main Modifications

by , | Sep 9, 2021 | Articles, Life Sciences, Patents, Pharma, Prosecution

At the end of 2020, the Brazilian PTO published Ordinance PR # 405 with new rules for presenting the Sequence Listing files as part of biotechnology patent applications. The transition from WIPO Standard ST.25 to Standard ST.26 takes effect globally on January 1, 2022.

The Brazilian PTO and IP offices abroad are taking internal measures to admit receipt of sequence listings in an XML-formatted file (eXtensible Markup Language), instead of a text file (.TXT). The WIPO Standard ST.26 was created to provide a universal format that facilitates data sharing. The main objectives of the new rules can be found here.

Regarding the main changes brought about by the new format, in addition to the presentation in XML, it is possible to highlight that the ST.26 clearly divides the data presented into two parts:

1. “General information of the patent application”

The main purpose of bibliographic information is to provide an association between the sequence listing with the patent application.

While the current standard allows the inclusion of all priority applications, all applicant names and only one title, ST.26 allows only the earliest priority and one applicant name; however, multiple invention titles are permitted, each in a different language.

2. “Biological sequence information”

The main purpose of biological sequence data is to provide one or more sequence elements, each of which contains information about one sequence. Sequence elements include various feature keys and subsequent qualifiers.
While the current standard identifies the molecules as DNA, RNA or PRT (protein) separately, ST.26 requires a mandatory qualifier to describe the molecule (“mol_type”), which can be DNA, RNA or AA (amino acid), wherein the AA sequences are represented only by the single letter code. Furthermore, ST.26 strictly defines the feature location in all sequences and allows the inclusion of additional types of sequences, such as nucleotide analogs and D-amino acids. Nucleotide sequences (DNA or RNA) with less than 10 nucleotides and AA sequences with less than 4 amino acids are prohibited with ST.26.

According to information provided by WIPO, the tool for authoring, editing, validating, and generating sequence listings in XML has an intuitive user interface. Projects can be saved in different formats and locations that can be imported and converted immediately.

Although the ST.26 appears to be a challenging change for patent applications, its implementation raises high expectations for better accessibility, classification and preservation of biological information described in the sequence listing worldwide.

Finally, despite the format being mandatory only in 2022, the voluntary submission of the Sequence Listing in the new format by the Applicant will be accepted by the Brazilian PTO during 2021.

We are pleased to inform you that DANIEL LAW has been invited by WIPO to join the WIPO Sequence Improvement Project testers group and assist in the development of the Sequence Listing software. Therefore, if you have any questions, please feel free to contact us. We will be glad to help you with this matter.

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