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.
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 to the NCBI FTP site and download the latest taxonomy files.
Just before connecting to the NCBI, BiSSAP displays a confirmation dialog.
If the computer is located behind a proxy, you will sometimes have to fill in values for the proxy settings (in "BiSSAP Preferences"). If in doubt, please consult your local network administrator.
Custom names
If you need to use a custom name, you must first add it to BiSSAP's taxonomy database (to avoid misspellings).
Adding a custom name via the Taxonomy Manager
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Select Tools -> Taxonomy Manager from main menu.
- BiSSAP opens the Taxonomy Manager window.
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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.
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If you need to change the name of the organism, or that of a translation table, click the Update
button. The name update dialog is displayed.
- To delete a name, simply select it and click the Delete button.
Adding a custom name via the Create Sequence dialog
You can add a new organism during sequence creation.
- Follow the usual sequence creation procedure.
- Enter the new name for your organism.
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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.
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If you accept, Create a new name dialog is displayed. Correct the translation code, if necessary.
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The new sequence and 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.