General

BiSSAP can export two different kinds of file format: drafts, which are temporary files, and final sequence listings, which are ready for submission to the patent office. This document describes how to generate and verify final sequence listings.

Generating sequence listings

To generate a final file for submission to a patent office:

  1. Right-click a project in the Project Browser.
  2. Select Generate Sequence Listing.

  3. Choose file format.

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  4. Choose the directory and name of the sequence listing file.

  5. If you want the generated file to be compressed as a zip file, make sure Compressed is checked.

  6. You can generate a PDF file in addition to the text file. Please check Generate PDF as well (this is active only when ST.25 is the chosen format).

  7. If the chosen output format is XML, you can generate a file with reference to a stylesheet for clearer layout. Click Include stylesheet box.

  8. Click Export Project to start the process.
  9. If the verification is successful, the sequence listing is generated. If not, a Report Viewer window will open with a list of errors and warnings.

While awaiting the results, you can start work on another project by clicking Run in the background.

After verification, the program asks you whether it should display the generated file.
Open summary question

If you answered yes to open verification summary, BiSSAP displays the generated sequence listing.

If you chose to include a stylesheet, BiSSAP also opens the stylesheet view in the internal browser.

Important:
The program performs verification before generating a sequence listing, and does not allow generation until any errors are fixed (see next section).

Verification and validation

BiSSAP supports validation and verification.

  • Validation is performed each time an editor or dialog is saved. It is also performed for each import to establish whether the data structure in the imported file is correct. The validation process also involves some pre-processing for verification purposes. The idea of this pre-processing is to show to you what is wrong with the input so that you can make the necessary corrections.
  • Verification deals with the structure of the documents, not with their content. When you run a verification routine, the data has been already read and put into data structures. You verify those data structures to see if the information they contain is correct and complete.

Sometimes the imported files contain errors. BiSSAP does not give up on incorrect files, but rather tries to recover as much of the data as possible. This means that users can import faulty data into the program, and then correct it (or simply accept the corrections BiSSAP makes while importing).

Each editor handles just one piece of information, e.g. a feature or sequence. You cannot save data that is plainly wrong in BiSSAP (or if you can, you have found a bug – please report it to the BiSSAP team at bissap@epo.org). Sometimes an automatic action triggers other changes, but it is assumed that the project will be verified as a whole at a later stage.

Verification is launched in two ways:

  • Generating a sequence listing file launches the verification routine just before the sequence listing file is written to disk.
  • You can launch verification by right-clicking the project name in the Project Browser, and then selecting Verify Project from the pop-up menu.

  • Changing or adding an object also launches the verification process.

If any errors are detected during verification,

  • BiSSAP displays the following error message:

  • BiSSAP opens a new view called Report Viewer. You can export the content of the Report Viewer to a file. Double-click any of those errors to open an editor in which to correct that error.

If there are no errors,

  • you will get the following message:

  • There can also be warnings, so check the Report Viewer as well.

Markings in the Project Browser and Sequence Browser

Each time an error or warning is discovered, the element in question is highlighted in the Project Browser or Sequence Browser. Not only is the element highlighted, but so too is each element between the root and the wrong element.

The markings are as follows:

  • errors are marked red
  • warnings are marked yellow

Error marks after verification

Disclaimer

The verification routine detects many of the common errors in sequence listings. However, it may not detect them all. Using BiSSAP does not guarantee that your sequence listing will be completely error-free. The correctness of the sequence listing, especially the biological data, remains your responsibility.