BiSSAP uses a controlled taxonomy. Not all organism names are appropriate for use in patent applications. Usually only scientific names are accepted.

BiSSAP supports the NCBI taxonomy list. However, the NCBI taxonomy contains 16 classes of names, like synonyms, GenBank common names, etc. These may or may not be acceptable depending on the rules, which are highly complex and go beyond the scope of this program.

In the BiSSAP Preferences, you can determine which name classes are active and which are included in the project verification.

Taxonomy preferences

The organism names are provided by way of guidance, but they should not be treated as a definitive listing.

If you use scientific names only, you can be sure that your sequence listing complies with the requirements as regards the sources of the sequences.

Taxonomy update

The NCBI updates the taxonomy every hour. If BiSSAP is running on a computer with internet access, it will connect once a day (default) to the NCBI FTP site and download the latest taxonomy files. You can set the frequency of BiSSAP taxonomy update (Daily, Weekly, Monthly) in BiSSAP Preferences.

Just before connecting to the NCBI, BiSSAP displays a confirmation dialog.

If the computer is located behind a proxy BiSSAP will try to read the proxy settings from the machine. In case it was not possible to read such settings, please fill in the values for the proxy settings in BiSSAP Preferences. If in doubt, please consult your local network administrator.

User-defined names

If you need to use a user-defined organism name, you must first add it to BiSSAP's taxonomy database (to avoid misspellings).

Adding a user-defined name via the Taxonomy Manager

  • Select Tools -> Taxonomy Manager from main menu.

  • BiSSAP opens the Taxonomy Manager window.

  • To add a new name, click the New button. The Create a new name dialog is displayed.

    For each name, select the protein translation table that will be used to generate proteins for that organism.
  • If you need to change the name or the value of the translation table of a user-defined organism name, select the organism name in the Taxonomy manager window and click the Edit button. The Organism name update dialog is displayed.

  • To delete a name, simply select it and click the Delete button.

Adding a user-defined organism name via the Create Sequence dialog

You can add a new organism name during sequence creation.

  • Follow the usual sequence creation procedure.
  • Enter the new name for your organism.

  • When you click Create sequence, BiSSAP displays a message telling you that such an organism does not exist in the BiSSAP database. You then choose whether to create an entry for that organism in your database, or return to the form and change the name.

  • If you accept, Create a new name dialog is displayed. Change the translation code, if necessary.

  • The new sequence and the new organism are created. You can see the organism in the Taxonomy Manager.

Follow the same procedure to edit a sequence. If you have entered a new name, BiSSAP will offer to add that name to the taxonomy database before you save the Sequence Editor content.

More information (NCBI)