WIPO Sequence

FAQ : Implementation of WIPO ST.26

General Questions

1: 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 an ST.26-compliant XML sequence listing required as a follow-on submission for earlier-filed applications?

Based on the recommendation for the transition provisions from Standard ST.25 to ST.26 presented by the 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 (international) filing date as the reference date, not the priority date; and

(c) July 1, 2022 as the transition date (see document CWS/6/15).

This means that all applications filed on or after July 1, 2022 containing amino acid and nucleotide sequences must contain an ST. 26 XML compliant sequence listing. Applications filed before that date disclosing one or more nucleotide and/or amino acid sequences, must contain a sequence listing compliant with WIPO Standard ST.25.

2: 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 application filing of original documents, 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.  For the international publication of a PCT application by the International Bureau, they will publish the ST.26 compliant sequence listing in XML format, as filed by the applicant, along with an application number that is encoded within the filename of batches (PCT-EDI batch filename).

However the general information part of the sequence listing will be published as submitted without correcting or adding any bibliographic data, e.g., the application number. A receiving Office or International Authority is not expected to edit ST.26 sequence listing files and the International Bureau strongly recommends that they do not edit them.  Sequence listings and other files are to be matched up by applicant references and ST.36 data.  The draft PCT Administrative Instructions indicate that even if inconsistencies are found between bibliographic data in the sequence listing and the equivalent data in the request or application body, the applicant should not be required to correct the sequence listing.  Instead the application will be processed on the basis of the bibliographic data from the request.

Questions on WIPO Sequence Suite

WIPO Sequence 

3: 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.

4: 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

5: 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.

6: 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. 

7: 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.

8: 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. 

9: 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 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

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

Currently, any newly improved versions of the WIPO Sequence Validator are published on the WIPO website and it is currently planned that all Offices will be informed of this new release by email. It should be noted that while it was initially planned to release a new version via auto-update, such as we have it for the WIPO Sequence, Offices indicated that they preferred to download and install it manually.

If Offices wish, the International Bureau may reconsider an auto-update solution depending on the expected update frequency, Office demand and available budget. If you have any suggestion, please let us know at wiposequence@wipo.int.

11: 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 after downloading the new release from the WIPO website. 

12: 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 ST.26 rules. 

13: In the WIPO Sequence Validator Operations Manual (for version 1.0.0 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) 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 just in a report folder. 

14: 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.

15: 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.

16: 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.

17: 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

18: If an Office is not ready to implement the new/modified PCT Forms (Request Form, etc.,) by the transition date, are they able to continue using the old forms? 

With respect to international applications filed before but processed after this date, the corresponding old Forms may still be used. In this sense, it is suggested that the Offices concerned will make both the old and new Forms available for a certain period of time so that the appropriate Forms may be used depending on the international filing date. If this is not technically feasible, the International Bureau would suggest that the Offices concerned use the new Forms for all cases and then make an appropriate note in the relevant Forms under “additional observations” or in a supplemental box to explain any specific points that should be pointed out as a result of using the new Form in an old case. For example, the note may specifically repeat the information that is available in an old Form but deleted in the new Form, or point out that a reference to WIPO Standard ST.26 (XML file) should be understood to be a reference to WIPO Standard ST.25 (text file), where the corresponding text is relevant.  Additionally, the respective Form Communication in Cases for Which No Other Form Is Applicable may also be used when necessary. The International Bureau aims to use the appropriate forms in ePCT and provide stylesheets that allow generating the relevant form content according to the context.

19: If applicants don't 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. Applicants are free to use any tool they wish as long as the resultant sequence listing complies with WIPO ST.26 at filing. 

According to the draft PCT Administrative Instructions, it is not required for a receiving Office (RO) to validate the sequence listing. However, they may do so if they wish.  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.

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 or a designated Office, 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 ST.26-compliant sequence listing. 

20: Will the International Bureau update the module(s) of the PCT-SAFE application to accommodate applicants being able to upload ST.26 XML file formats for sequence listings that will accompany the PCT application? Currently it only accepts ST.25 format.

Yes, PCT-SAFE, ePCT and the PCT module within eOLF will be updated to allow WIPO ST.26 ('.xml') uploads from July 1, 2022. Furthermore, the ST.25 upload will be switched off in PCT-SAFE because PCT-SAFE only handles the initial filing.  ePCT will allow WIPO ST.26 for new applications and ST.25 for subsequently filed documents based on applications filed before 2022.

As of July 1, 2022 the drop-down menu file filter for the sequence listing part of the description will no longer display the *app and *txt options. Instead it will only offer the possibility to attach an *xml sequence listing file.  There will be other modifications – which are still to be determined – such as new DTDs, file codes, stylesheets, etc.  As the filing DTD package will be modified to support ST.26 sequence listings, the receiving Office receiving servers will need to be updated well before July 2022.  The International Bureau will coordinate with the Office to ensure that their servers are ready before the end of 2021.

PCT-SAFE will probably carry out only very basic checks, which is similar to the “sanity check” that is done on ST.25 files, checking for convincing tags in the first few lines of the file rather than a full validation.  Applicants using old versions of the client will find that it accepts ST.25 files only and not ST.26 files. 

It is intended to make the relevant changes in the July 2021 release of PCT-SAFE, so the new arrangement should become available from July 1, 2022 for any applicant using that version or later.

21: If a non-compliant sequence listing is filed with a new application under the PCT System, how long does the applicant have to remedy this? 

In most cases, the receiving Office will neither check the format and contents of sequence listings, nor invite correction of defects.  In most cases, defects will be recognized only by the International Searching Authority.  In this case, the normal course of action will be to invite the applicant to furnish a listing under Rule 13ter for the purposes of international search.  That listing will not form part of the international application.  Although it will be possible for the applicant to seek to amend the application under Article 34 if international preliminary examination is demanded (or possibly to correct or rectify the defect), in most cases, correction of the defect will need to take place in the national phase, according to the deadlines that apply there.

In the (unusual) case where the receiving Office invites the applicant to correct a defect in format of the sequence listing, the usual time limit under Rule 26.2 of two months from the date of the invitation will apply.

22: Will the International Bureau be removing the ST.25 file upload capability when they migrate over to ST.26 file upload capability at 'big bang' ?

The ability to attach an ST.25 file to an application at filing will disappear overnight in ePCT and, to the extent that people are using an up-to-date version where ST.26 is recognized, in PCT-SAFE.  PCT-SAFE doesn’t track subsequently filed documents.  ePCT will continue to allow ST.25 files to be uploaded as SFDs for pre-2022 international applications.

23: Will there be a new document code for the ST.26 XML file type uploaded via PCT-SAFE? 

This has not been decided.  However the International Bureau assumes that the document code for filename bodies will likely be unchanged.  Of course, file extensions will be .xml and there will also be some changes in XML referencing files, notably in some XML (such as in the ST.36 <sequence-list>) where currently a fixed attribute of 'ST.25' is used.  The final decision will be announced shortly.

24: 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), ROs will continue to be required to permit the filing of international applications on paper."

Which of the following cases are considered as international applications on paper:

(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))

PCT/WG/13/8 refers to both of those cases.  For the accordance of a date of filing, it is sufficient for an applicant to file a description and a set of claims.  Where the description contains sequences that are supposed to be presented as part of a sequence listing, that is a formal defect, but it is one that the receiving Office may well not notice and, even if it did, in many cases it would be impractical to deal with it as a correction.  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 that is actually part of the description as a matter for possible amendment in the national phase.

25: In the case of either Question 24 (i) or (ii) above, may the receiving Office accord the international filing date for such an application? After filing such an application, may applicants incorporate a sequence listing into the application/description as one forming part of the application/description by completion of the missing "sequence listing" part (Rule 20.5; in such a case, the international filing date is corrected), or incorporation by reference or Article 34 amendments (in such cases, the international filing date may be maintained)?

Yes.  If all the requirements of under Article 11 PCT are met, the receiving Office will accord a filing date.  Article 11 requires the application to have "a part which on the face of it appears to be a description". The fact that the sequence listing is missing does not prevent the accordance of a filing date. Whether a sequence listing can be incorporated by reference under Rule 20.6 PCT is upon the receiving Office to decide. Furthermore, an applicant may submit a sequence listing for the purposes of the international search under Rule 13ter. 

26: Under PCT Regulations Rule 89bis.1(a) : 

(i) Shall an international application on paper under Rule 89bis.1(a) be treated as an application (the description of) which does not include the sequence listing (part of the description)? If so, does the application violate Rule 5.2(a)? Especially in case of Question 24 (i), how should the sequence listing on paper be treated? Is it treated as a part of the description? 

Yes, an application entirely on paper (not accompanied by a sequence listing in electronic format) containing sequences that are supposed to be included in a sequence listing are automatically contrary to Rule 5.2(a).  Details of this will be provided in the PCT Administrative Instructions, but the International Bureau recommends that the receiving Office should review the entire application, including the sheets containing sequences, for proper physical requirements set forth in the receiving Office Guidelines and then pass it to the ISA for search without further comment.  The ISA will then, if the listing is needed to perform a search, request a sequence listing under Rule 13ter.

(ii) 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 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.  

(iii) 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", which is 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" instead only part of the file that is accessible as from 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.

(iv) 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 by incorporation by reference (Rule 20.5, 20.6)? Can applicants amend the description to include the sequence listing part (Article 34(2)(b))?)

Under particular circumstances that are to be decided by the receiving Office, 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 unless the listing was included in a priority application), or by 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. Introduction of the sequence listing as a rectification before the ISA or IPEA might be possible in some limited cases, but ROs will not be able to consider introduction of the listing as a correction.

The normal case for international applications where a sequence listing should have been filed but was not is that the ISA will require a sequence listing for the purpose of search under Rule 13ter.

(v) 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.

27: Sequence listings provided in a non-compliant ST.26 format or with language-dependent free text in a language not accepted by the receiving Office (e.g., ST.25 sequence listing): 

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

An ST.25 sequence listing or images (e.g., PDF) would definitely be contrary to Rule 5.2(a) and, while these would need to be recognized as part of the description as filed, they should not be treated as "the sequence listing part of the description".  A sequence listing that appears to be valid ST.26 but has incorrect language for the free text would best be treated as being a sequence listing part of the description even though there are defects.  The particular case of incorrect language may be best dealt with by requiring a translation of the listing under Rule 12(3), rather than expecting the receiving Office to request a correction of the formalities defect.

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

Yes. The status of the later filed sequence listing would depend on whether the applicant chose to provide a Rule 12 translation or Rule 13ter listing for the purpose of search.

(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.  They are generally delivered as "communication on request" under Rule 93bis, so that it is a matter for the individual Offices to decide whether they retrieve them or not.

28: A PCT application is filed on July 1, 2020 with an ST.25 sequence listing and then after entering national phase (e.g. at the EPO) a divisional application is filed on or after July 1, 2022. Will the applicant have to file a ST.26-compliant sequence listing for the divisional application, or is it possible to use the ST.25 sequence listing, filed in the (international) parent application?

This is a matter of national law.  However, the recommendation (following extensive discussion among Offices of the desire to switch to ST.26 as quickly as possible) is that since the date of receipt of the divisional application is after the big-bang date of July 1, 2022 the sequence listing for the divisional application should be compliant with WIPO ST.26.

National/Regional filings

29: Where do Offices find out what is expected from each National Office to implement 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 has prepared a training webinar series for staff in IP Offices and for end users, which will be provided as a series of recorded Webinars published on the WIPO website.  Registration and recordings can be found at: https://www.wipo.int/meetings/en/topic_bodies.jsp?group_id=330 

Offices can contact the International Bureau with their particular requests including those for test data at wiposequence@wipo.int . 

30: 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 effective transition to ST.26, it is recommended that the divisional sequence listing be filed in ST.26 format on or after July 1, 2022 if a parent application has a sequence listing provided in 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 ST.26 compliant. Offices should consider their practice when carrying out their ST.26 implementation plan during 2021. 

31: 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 priority? Also will amendments to the filed non-compliant sequence listing, to provide an 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 provided.  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 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.

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

32: 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 this 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.

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

Yes, you will need to convert the sequence listing to ST.26 for use as part of the description in the later PCT application filed on/after July 1, 2022.  However, there is no need to convert the sequence listing in the priority document as such.  That should remain in the ST.25 format in which it was originally filed.