BiSSAP can generate output files in a number of different formats from an existing project. The official WIPO formats are described in detail elsewhere in this User Guide, and descriptions are also available on the WIPO website. This page provides short summaries of all the formats supported by BiSSAP, and describes how each format fits into the BiSSAP workflow.

.bis files

Description

These are draft files intended for internal exchange within your company or other similar situations. They look like XML files, but are in fact a proprietary BiSSAP format. Do not send these files to a patent office.

BiSSAP does not allow you to generate sequence listings that contain serious errors, or listings that are obviously incomplete. However, this can be a problem if you need to transfer incomplete or erroneous data to a different BiSSAP installation. Draft files have been introduced for this very purpose.

Draft files may be incomplete, as there is no verification at the export stage.

This BiSSAP format is designed for short-term usage. The compatibility of files between versions is not guaranteed in the long run (especially until the beta-testing period is over), so do not use this format for long-term archiving.

Generation

To generate .bis files:

  • Select the project in the browser and right-click it.
  • Choose Export as Draft.

  • Choose the file name. The extension will be added automatically.

  • The application asks if you want to see the generated file.

  • If you answered yes, the file is opened in the workbench.

.xml files (XML)

To generate these files, choose Generate Sequence Listing from the menu and then XML from a drop-down list of possible formats. These are the real sequence listing files that you are going to deliver to the patent office.

These files can also be generated as a compressed .zip archive.

.st25 files (ST.25)

To generate these files, choose Generate Sequence Listing from the menu, and then ST.25 from a drop-down list of possible formats. These are the real sequence listing files that you are going to deliver to the patent office.

These files can also be generated as a compressed .zip archive.

Export formats

BiSSAP also supports the exporting of individual sequences to a file. This feature is designed to help you to use the exported sequence from a sequence listing in other software, including software that does not support the sequence listing XML or ST.25 formats.

In addition to the .xml and .st25 files, BiSSAP supports export to:

  • EMBL
  • FASTA

Backup files

These files contain a backup of the entire internal database as an SQL file. They are for temporary backup only, i.e. they are not drafts, and should NOT be submitted to a patent office.

The backup file can only be restored with 100% safety in the version of BiSSAP with which it was generated. As BiSSAP is not designed for long-term data storage, the backup is intended only for temporary protection. No migration procedure is planned.

The situation with ST.25 (.st25, .txt) and XML files (.xml) is totally different: these are standard formats that each version will be able to read and write. When you complete a project and generate one of these files, you can be confident that any subsequent version of BiSSAP that supports these formats will be able to read them.