FAQ : Implementation of WIPO ST.26

General Questions

1: What is "big-bang date"?

The “big bang date” refers to the date on which Offices at the national, regional and international levels should simultaneously implement WIPO Standard ST.26. It has been set as July 1, 2022, but check with your national Office for any specific local details regarding this.

2: Do only new applications which include sequence listings filed on or after July 1, 2022 have to contain an ST.26-compliant XML sequence listing, or is a WIPO ST.26-compliant XML sequence listing required as a follow-on submission for earlier-filed applications?

Based on recommendations for the transition provisions from WIPO Standard ST.25 to ST.26 presented by the CWS Sequence Listing Task Force, the Committee on WIPO Standards (CWS) reached an agreement on:

(a) the “big bang” scenario as the option for the transition for all IPOs, meaning that Standard ST.25 no longer applies for international applications filed as of July 1, 2022;

(b) the filing date as the reference date, not the priority date; and

(c) July 1, 2022 as the transition date (see document A/62/12).

This means that all applications filed on or after July 1, 2022 disclosing amino acid and nucleotide sequences must contain an ST.26 XML compliant sequence listing. Any sequence listing furnished in respect of any applications filed before that date should still comply with WIPO Standard ST.25, even if the sequence listing is submitted after (for example in amendments or translations for PCT national phase entry).

3: How can the applicant prepare a sequence listing that is ST.26-compliant?

WIPO provides a desktop tool called “WIPO Sequence” that enables patent applicants to prepare amino acid and nucleotide sequence listings compliant with WIPO Standard ST.26, as part of a national or international patent application. This tool is provided for three operating systems: Windows, Mac OS and Linux. For further information, please refer to the WIPO Sequence homepage.

Applicants are free to use any XML-editing tool they wish to produce the sequence listing as long as it complies with WIPO Standard ST.26 at the time of filing.  However, WIPO ST.26 is complicated and it is strongly recommended only to use software specifically designed for this purpose.

4: If Offices want to publish a sequence listing submitted as a ST.26 XML formatted file, do they need to publish the entire contents of the XML file (including XML schema identifiers), in order to be compliant with filing of original documents at application, or can they 'strip-out' the XML tags, leaving only the sequence listing content (i.e., in a human readable format)?

This is a decision for the Office, according to their own national law and practice, but the XML format will in most cases be the most useful to patent information users.

For the international publication of a PCT application by the International Bureau, the ST.26-compliant sequence listing in XML format, as filed by the applicant, will be published. Additional information (including the international application number) will be provided as associated metadata on the associated web pages, referring XML files and filenames, not by editing the sequence listing itself.

WIPO Sequence Suite

WIPO Sequence Suite

5: What is the WIPO Sequence Suite?

The WIPO Sequence Suite are two associated tools developed by WIPO to support applicants and Offices to adopt use of WIPO Standard ST.26 on or after the implementation date of July 1, 2022. The first is WIPO Sequence: a desktop tool that supports applicants in authoring and validating sequence listing information in order to generate a WIPO ST.26-compliant sequence listing. The second is the WIPO Sequence Validator: a web service which is incorporated into patent Office environments to allow them to check the compliance of filed sequence listings against WIPO Standard ST.26.

6: Will the full validation within WIPO Sequence be to the same standard as the full validation within WIPO Sequence Validator ?

There are only minor differences between the validation process for the WIPO Sequence and the WIPO Sequence Validator. For example, the desktop tool might respond with an 'Error' where the Validator tool might respond with a 'Warning'.  This allows an IP Office to have flexibility in its treatment of sequence listings that have certain errors.

7: Can an applicant import an ST.26 XML file into WIPO Sequence from a storage medium, such as DVD? 

Yes, the desktop tool will allow the user to navigate to any file location/storage medium to retrieve a file for import.  For further guidance see the WIPO Sequence User Manual

8: Can individual sequences be printed once created or imported into a project within WIPO Sequence? 

Yes, there is a print functionality within the desktop tool which supports the printing of sequences.  For further guidance see the WIPO Sequence User Manual.

9: Can the WIPO Sequence be used without an internet connection?

Yes. WIPO Sequence has been implemented as a stand-alone desktop tool, as opposed to a web application so that applicants can work without being connected to the internet.  However, in order to ensure that you have the latest version, by invoking the auto-update feature work, it is necessary that you are connected to the internet. Additionally the software architecture also provides the potential for the desktop tool implementation to be deployed as a web application in the future. 

10: What font sets are used by the WIPO Sequence? 

  • Default: Roboto-Regular/Roboto-Medium.ttf;
  • Arabic: LateefGR-Regular.ttf;
  • Chinese: KaigenSerifTC-Regular.ttf/KaigenSerifTC-Bold.ttf;
  • Japanese: Ipam.ttf/Ipag.ttf; and
  • Korean: KaigenSansK-Regular.ttf/KaigenSansK-Medium.ttf.

11: Where is the list of organisms provided in the WIPO Sequence derived from? 

There are currently two sources for the list of organisms names: the pre-defined list of organisms derived from two industry databases, provided by the International Bureau and local list of custom organisms that are stored in the WIPO Sequence instance by the user. 

The pre-defined list of organisms is updated annually and is derived from the scientific names at the species level and at the genus level as listed in the Integrated Taxonomic Information System (ITIS) database and in the International Committee on Taxonomy of Viruses (ICTV) Master Species List. 

Finally, the custom organisms which are stored on the local machine will also appear as part of the organisms list shown in the tool. Currently, the names of the custom organisms included in a sequence listings are not shared with the International Bureau. The International Bureau is currently in discussion with the Sequence Listings Task Force about how custom organisms could be incorporated, after review, into the pre-defined list. 

12: From reading the ST.26 Document Type Definition (DTD), it appears that ELEMENT “INSDSeq_other-seqids” and its child element “INSDSeqid” will be added by the Office, so it cannot be generated from the desktop tool. Is this correct?

Yes, this is correct.  While a preferred format for this particular sequence ID is defined in the ST.26 DTD, it is not generated by the tool.  In fact, there is a verification rule that ensures that this element is not present in the XML. This field is intended for the use of IP Offices which exchange sequence listings with database providers only and not for data communicated between IP Offices. For further details see Annex V of WIPO Standard ST.26.

Format:
pat|{office code}|{publication number}|{document kind code}|{Sequence identification number}

where office code is the ST.3 two-letter code of the IP office publishing the patent document, publication number is the publication number of the application or patent, document kind code is the letter codes to distinguish patent documents as defined in ST.16 and Sequence identification number is the number of the sequence in that application or patent.

Example:
pat|WO|2013999999|A1|123456

WIPO Sequence Validator

13: If there are updates to the WIPO Sequence Validator, how does the International Bureau plan to distribute these to the National Offices? 

Currently the International Bureau will contact IP Offices by email to inform them of a new WIPO Sequence Validator release. Offices are encouraged to inform the International Bureau of their email addresses for correspondence regarding the WIPO Sequence Validator.

14: Is this the same process for new users of the WIPO Sequence Validator?

Yes. Offices which have already installed the Validator and new users of the Validator will both have to replace the existing WAR/JAR file when the International Bureau distributes the latest version to them. 

If an IPO deploys the service as a WAR, the original configuration settings within the Apache Tomcat configuration file can be reused once the application server is restarted. Equally for the Spring Boot JAR service, configuration can be externalized as a .conf file. Further details are provided in the WIPO Sequence Validator operations manual.

15: The WIPO Sequence Validator provides two types of validation: 'formality' and 'full'. What are the differences between these two validation types? How shall these validation types be used by Offices? 

The 'formality' validation checks that the file format is in XML format and that it is compliant with the ST.26 Document Type Definition (DTD).  The 'full' validation commences with the formality validation check and then also checks compliance with a series of verification rules derived from WIPO ST.26.

Each sequence listing has to go through a full validation but the formalities validation, performed by the Validator, could form a step in the e-filing process to provide prompt feedback to applicants at the time of filing.  The full validation check, depending on the size of the sequence listing, could take a significant time so may not be suitable for integration in these e-filing systems.  Therefore, the full validation could be conducted later in a batch process by the Offices.

A 'formality' (only) validation may be sufficient for a filing in some cases, however a 'full' validation is almost certainly required to ensure a compliance with WIPO ST.26 rules. 

16: In the WIPO Sequence Validator Operations Manual (for version 1.1.0 of the tool), it states in the "Validate XML File" use case that the web service client can request 'full' or 'formality' validation. Is the client here the applicant or the IT system requesting the validation? 

Here the 'client' is the Office's IT system as every sequence listing has to go through 'full' validation in order to ensure compliance with WIPO ST.26.

The latest improvement of the Validator Tool version (WAR & JAR) in version 1.1.0 allows an end point to make a call to the Validator web service and receive a response which includes the verification report, instead of providing the client this report in the specified report folder. 

17: In what manner does the International Bureau expect National Offices to inform applicants of the results after verification of filed sequence listings (ST.26 XML files) by the WIPO Sequence Validator, for both the 'formality' validation and the 'full' validation?

The WIPO Sequence Validator was developed so that all Offices would be able to produce the same verification reports after validation process of the same sequence listing. It is recommended that the verification report provided by the Validator is sent "as is" to the applicant.  The WIPO Sequence Validator has been developed with configurable error messages so these can be improved in future versions to be more meaningful to the applicant, not just the Offices, based on any feedback received by the International Bureau.

18: Does the International Bureau envisage a receiving Office to be responsible for verifying a sequence listing which is part of a PCT application, using the WIPO Sequence Validator tool, or is this expected to be carried out by the International Bureau/International Searching Authority? 

There is no obligation or requirement for a receiving Office to validate a ST.26 sequence listing prior to forwarding the application onto the International Bureau. However it is recommended, where possible, to ensure that the Office’s eFiling systems validate these files before they are formally submitted so that the applicant can be warned of potential defects at the earliest moment.

It should be noted that at this stage, there is no requirement for Offices to report back to applicants any problems regarding their sequence listing. If needed, however it is recommended that Offices provide them with the verification report produced by the WIPO Sequence Validator, which should be sent as is.

19: If the WIPO Sequence Validator reports errors for a sequence listing during a 'full' validation request, are Offices expected to correct the errors on behalf of the applicant by editing the ST.26 XML file?

Even though it is up to the competent Office, generally Offices would not be expected to edit the sequence listing file.

20: Has the International Bureau set a continuous improvement process in place for the WIPO Sequence Validator?

The International Bureau plans to continually improve the Validator as required. Currently, during this development period in 2021, Offices provide their suggestions for improvement which are logged, prioritized and scheduled for implementation. The International Bureau will review this process with Offices and adapt to establish a formal process which should be part of the support model for the WIPO Sequence Suite.

PCT filings

21: If applicants do not use the WIPO Sequence to create the ST.26 XML file for the sequence listing, are Offices still obliged to validate the sequence listing, using the WIPO Sequence Validator tool?

As it is not mandatory for applicants to use WIPO Sequence to generate a compliant sequence listing, it is necessary to validate sequence listings following submission, to ensure they are compliant with WIPO ST.26. 

For International applications, according to the PCT Administrative Instructions (see paragraph 27 of Annex C), it is not required for a receiving Office (RO) to validate the sequence listing. However, they may do so if they wish. In any case, the International Searching Authority or the International Preliminary Examining Authority shall check the compliance with WIPO Standard ST.26.

If a receiving Office decides not to validate the received sequence listing and it is found to be non-compliant later by the ISA/IPEA, the applicant may be required to furnish a compliant sequence listing for the purposes of international search or international preliminary examination. The applicant may choose to address the defect by a filing compliant sequence listing as amendments under Article 34 in the international phase. Otherwise, the deficiencies reported may need to be remedied in the national phase, according to the provisions under the respective national laws. Each designated or elected Office can determine the allowable time-period for applicants to provide the WIPO ST.26-compliant sequence listing. 

Moreover, if an Office provides automated validation in conjunction with the uploading of the sequence listing XML file to an application filing system, the applicant would be made aware of defects that could potentially be fixed prior to formal filing of the application.

22: Will the International Bureau update ePCT to allow applicants to upload ST.26 XML file formats for sequence listings? Currently it only accepts WIPO ST.25 format.

Yes. ePCT will be updated to allow WIPO ST.26 compliant ('.xml') sequence listings to be uploaded from July 1, 2022.  As of July 1, 2022, the file format options for the sequence listing part of the description will no longer include *app and *txt, except for post-filing submission of sequence listings in relation to international applications filed prior to that date.  The only accepted format will be *xml (it will also be possible to attach a *zip file). 

The International Bureau is assisting receiving Offices with the modifications to their e-filing software and the technical preparations on their filing servers.

23: If a sequence listing filed with a new international application contains a formal defect, how long does the applicant have to remedy this? 

In the (unusual) case where the receiving Office invites the applicant to correct a defect in the sequence listing, the usual time limit under Rule 26.2 of two months from the date of the invitation will apply. In other cases, namely, where the receiving Office does not invite for correction, the applicant does not have to remedy the defect in the international phase and may leave the matter to be addressed in the national phase, according to the applicable national laws. Note also that, where the sequence listing furnished at the time of filing is not compliant with WIPO Standard ST.26, the applicant may be required to furnish a compliant sequence listing for the purposes of international search or international preliminary examination.

Details on how to file a corrected or rectified sequence listing are covered under paragraphs 33-36 of Annex C of the PCT Administrative Instructions.

24: Will the International Bureau be removing the WIPO ST.25 file upload capability when they migrate over to ST.26 file upload capability ('big bang')?

The ability to attach a WIPO ST.25 file to an application at filing will disappear overnight in ePCT. The sequence listing part of the description must be filed in WIPO ST.26 .xml format. For international applications filed before July 1, 2022, it will continue to be possible, on or after July 1, 2022, to upload in ePCT sequence listings in WIPO ST.25 format as subsequently filed documents, e.g., sequence listings under Rule 13ter or as rectifications or amendments. The current documents types in ePCT will continue to be used without any distinction between WIPO Standard ST.25 or ST.26 format.  

25: In paragraph 11 of document PCT/WG/13/8, which contains the amendments to the Regulations under the PCT for implementation of ST.26, it is stated that "in accordance with Rule 89bis.1(a), receiving Offices will continue to be required to permit the filing of international applications on paper". What will happen with the following two cases filed after July 1 2022?

(i) an application with the main part of the description, etc., on paper and a sequence listing also on paper (which might be a print-out of ST.26 XML or the like), without physical media on which ST.26 sequence listing file is stored; or

(ii) an application with the main part of the description, etc. on paper only, without sequence listing in any form?

(In both cases, assume that those applications are, under normal conditions, required to include the sequence listing part under Rule 5.2(a))

For the accordance of a date of filing, it is sufficient for an applicant to file a description and a set of claims. 

For both of the two cases cited above, where the description contains sequences that are supposed to be presented as a separate sequence listing in XML format and the sequences appear only in paper format (whether as a printout of an XML listing or showing the sequences in a different way),  the most likely way forward would be for the International Searching Authority (ISA) to request a sequence listing under Rule 13ter and leave the question of the lack of a sequence listing in XML format as a matter for possible amendment in the national phase.

For further details on how to handle sequence listings filed on physical media or when the application is filed on paper while the sequence listing is provided in electronic format, please refer to paragraphs 23-25 of Annex C of the PCT Administrative Instructions.

26:  In the case of a missing part being a WIPO ST.26-compliant sequence listing, after filing such an application, can applicants submit a WIPO ST. 26-compliant sequence listing under PCT Rule 20.5 (the international filing date is corrected) or Rule 20.6 (incorporation by reference)?  

The procedures of correction and incorporation by reference also apply to the sequence listing part of the international application. The applicant can submit a sequence listing complying with WIPO Standard ST.26 as a missing part to correct the international application or request it to be incorporated by reference, but it will be up to the receiving Office to decide whether a sequence listing can be incorporated by reference under PCT Rule 20.6, or accepted under PCT Rule 20.5.  

Alternatively, provided the sequences were sufficiently disclosed in the description, an applicant may submit a sequence listing for the purposes of the international search under Rule 13ter and correct the defect itself in the national phase. 

27: In a case where an applicant furnishes a sequence listing in a proper form and language in response to the invitation by the ISA under Rule 13ter.1(a), is the furnished sequence listing ("13ter sequence listing") treated only as one not forming part of the application/description (Rule 13ter.1(e))?

That is correct.  A Rule 13ter listing is not part of the description and considered furnished for the purpose of the international search only.  

(i) While Section 513(e)(ii) of Administrative Instructions provides that a "13ter sequence listing" shall be transmitted to the International Bureau, is such a "13ter sequence listing", when transmitted to the International Bureau, published as a part of the international publication? Is the "13ter sequence listing" transmitted to designated/elected Offices?

A Rule 13ter sequence listing is made available on PATENTSCOPE in a very similar way to sequence listing that forms part of the application (including rectifications and corrections).  It is not formally part of "the international publication" but instead only part of the file that is accessible as of the date of international publication. However it is available to designated Offices in exactly the same manner as a Rule 13ter sequence listing is at present. 

The International Bureau will be happy to give individual advice to concerned Offices taking into account their specific means of retrieval of national phase documents.

(ii) Do applicants have an opportunity to incorporate an ST.26 sequence listing into the application/description after the filing? i.e., may applicants furnish an ST.26 sequence listing to complete the  missing part or correct an erroneously filed, with or without incorporation by reference (Rules 20.5, 20.5bis, 20.6)? Can applicants amend the description to include the sequence listing part (Article 34(2)(b))?)

The applicant may have the possibility to introduce a sequence listing into the application either as a “missing part” (which will involve changing the filing date), or under incorporation by reference (provided that the sequence listing was completely contained in the priority application). The applicant may also furnish a sequence listing as an Article 34 amendment in Chapter II where the matter can be considered by an examiner, if the substance of the sequence listing was included in the description as filed. 

(iii) When a ST.26 sequence listing is furnished under Rule 13ter subsequently to the filing of the application, for the purposes of the international search or international preliminary examination, would the date of submission of the ST.26 sequence listing become the international filing date?

No, because a Rule 13ter listing does not form part of the international application. However, it should be noted that the ST.26 sequence listing must not go beyond the disclosure in the international application as filed and must be accompanied by a statement to that effect, e.g., “I hereby declare that the sequence listing does not go beyond the content of the application as filed”. Any such sequence listing shall contain only those sequences that were disclosed in the international application as filed.

28: A sequence listing is provided in a non-ST.26-compliant format or with language-dependent free text in a language not accepted by the receiving Office (e.g., WIPO Standard ST.25 sequence listing): 

(i) Shall it be treated as the sequence listing part of the description? If so, does such an application comply with Rule 5.2(a)? Are any corrections required?

A WIPO Standard ST.25 sequence listing would not satisfy Rule 5.2(a) and, while it may be recognized as the main part of the description if it is filed at the time of filing, would not be a "sequence listing part of the description complying with the Standard provided for in the Administrative Instructions".  It cannot be changed into ST.26 format as a correction of formality defect before the receiving Office.  Any ST.26 sequence listing provided subsequent to filing would lead to a later international filing date if it is intended to form part of the description, or otherwise may serve for search purposes only under Rule 13ter

A sequence listing furnished at the time of filing that appears to be compliant with WIPO Standard ST.26 but has incorrect language for the free text should be treated as being a sequence listing part of the description even though there are defects. Where the problem is detected by the receiving Office, the Office may transfer the international application to the receiving Office of the International Bureau (RO/IB) under Rule 19.4 if it is not prepared to deal with that language.  The receiving Office (either the original Office or RO/IB) may request a translation of the listing under Rule 12.3 or 12.4, just as would be the case for language defects in the main body of the application.  However, since the receiving Office is not required to check the sequence listing, the problem may only be detected by the International Searching Authority. In this case, the most likely solution would be for the ISA to request a sequence listing under Rule 13ter with the correct language free text.  National Offices could require translations to be provided formally on national phase entry.

(ii) For such an application, shall a "13ter sequence listing" (in WIPO ST.26 XML format), furnished in response to invitation by an International Searching Authority, be treated as not forming part of the application/description?

Yes. The status of the later filed sequence listing would be treated as a sequence listing but not forming part of the application.

(iii) Is such a "13ter sequence listing" published as a part of the international publication? Is such a "13ter sequence listing" transmitted to Designated/Elected Offices?

A Rule 13ter listing including a translation would be made available to the public at the same time as the international publication, but not formally be a part of the publication.  The Rule 13ter listings, assuming that they have been correctly transmitted to the International Bureau, are made available to designated and elected Offices on PATENTSCOPE. It is up to the individual Offices to decide whether they retrieve them or not.

29: If an applicant claims priority from an application with a WIPO ST.25 sequence listing, is it necessary to convert that sequence listing to WIPO ST.26 format if the PCT filing date is after July 1, 2022? 

The applicant will need to transform the ST.25 sequence listing filed alongside the priority application to WIPO ST.26 format, and potentially further update it for use as part of the description in the later PCT application filed on or after July 1, 2022.  WIPO ST.26 Annex VII provides recommendations on how to transform WIPO ST.25-compliant sequence listings to WIPO ST.26 format without introducing new matter.  However, there is no need to convert the sequence listing in the priority document as such. That should remain in the WIPO ST.25 format in which it was originally filed.

National filings

30: Where do Offices find out what is expected from each National Office to implement WIPO Standard ST.26? Are there any more detailed requirements on what National Offices need to do with the tools for example?

Each Office will have their own responsibilities towards their applicants; this is advice provided by the International Bureau.  

However, the International Bureau presented a training webinar series for staff in IP Offices and for end users on WIPO Standard ST.26, which was recorded and published on the WIPO website.

Offices can contact the International Bureau with any further requests for general training.

31: Do sequence listings need to be filed again when a divisional application is made?

This is a matter of national law. However taking into account the spirit of an effective transition to WIPO ST.26, it is recommended that the divisional sequence listing be filed in WIPO ST.26 format, on or after July 1, 2022, if a parent application has a sequence listing provided in WIPO ST.25 format.

As this is a decision for the Office, some may decide applicants to be allowed to “carry over” the sequence listing from the parent application to the divisional or request that applicants file a new sequence listing that is WIPO ST.26 compliant. Offices should consider their practice when carrying out their WIPO ST.26 implementation plan during 2021. 

32: Can a non-compliant sequence listing filed with a new application be considered to disclose the subject matter contained within it for the purposes of claiming priority? Also will amendments to the filed non-compliant sequence listing, to provide a WIPO ST.26-compliant file, not constitute added matters?

This is a matter of Offices' regulation and practices to handle non-compliant applications.  

It is recommended that everything in the application be looked at to determine whether 'added matter' has been included.  This would need to be considered on a case-by-case basis, as it depends on what was contained in the original description as well as the non-compliant sequence listing. In particular, mandatory qualifier annotations defined in WIPO ST.26 would be the 'sticking point'. If an application is submitted without a formal sequence listing, in order to avoid adding new matter, it should be a requirement that any such features are disclosed elsewhere in the application as filed. In principle, the presentation of a sequence listing in WIPO Standard ST.26 format should not in itelf be considered as adding new matter over the presentation of the same sequence listing in WIPO Standard ST.25 format. 

If the non-compliant sequence listing is in WIPO ST.25 format, WIPO ST.26 Annex VII should be consulted on how to transform a WIPO ST.25 sequence listing to a WIPO ST.26 sequence listing without adding subject matter.

33: If the application is filed before July 1, 2022, but without a sequence listing, in which format should the sequence listing be filed as late-filed document if requested after July 1, 2022?

As the filing date is prior to July 1, 2022 the sequence listing should be filed in WIPO ST.25 format.

For national or regional application, this is a matter of national law. Applicants should consult with the competent Office.