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USPTO Proposes New Standard for the Disclosure of Sequence Listings Using XML   Leave a comment

In an announcement in the Federal Register on May 15, the USPTO posted a request for comments on the recommendation for the disclosure of sequence listings using XML (Proposed ST.26).   The standard is being revised to require the use of extensible mark-up language (XML) format, to update the standard, and to more closely align requirements of the standard with those of public sequence database providers.  The USPTO is requesting comments to be received on or before July 16, 2012.  No public hearing will be held.

As an explanation for the proposed change, the USPTO explains that in October 2010, the Committee on WIPO Standards (CWS) established a Task Force, designating the European Patent Organization (EPO) as the lead, to propose a revised standard for the filing of nucleotide and/or amino acid sequence listings in XML format, known as the “XML standard.”  It is expected that the XML standard will be adopted at a meeting of the CWS in early 2013.

The text of the current draft of the proposed main body of the sequence listing standard, with its associated Annexes, is available via the Office’s Web site: click here.  The documents are also available below:

1. Recommendation for the disclosure of sequence listings using XML (ST. 26): click here.

2. Annex B1 Controlled Vocabularies: click here.

3. Document Type Definition (DTD for ST. 26): click here.

Some of the highlights of the proposed changes include:

1. The XML standard (paragraph 4) prohibits the inclusion of any branched nucleotide or amino acid sequences or any sequences with fewer than ten specifically defined nucleotides or fewer than four specifically definted amino acids.

2. The XML standard (paragraph 5) specifies inclusion of sequences containing any nucleotides that can be represented using any of the symbols set forth in Annex B.1, paragraph 1, Table 1.  This includes modified nucleotides.

3. The XML standard (paragraph 6) specifies the inclusion of sequences containing D-amino acids.

It remains to be seen how this new XML standard will impact biotech practice, and how burdensome it will turn out to be, or how useful.


Posted June 13, 2012 by deboraplehn in USPTO

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