Frequently Asked Questions

The database also contains some of the dictionaries used by the program, e.g. for country names or organisms. It is not generally possible to edit the dictionaries.

BiSSAP cannot write entries to the database that are totally wrong. However, the database may in some cases contain incomplete information.

How do I delete an object (ie, a sequence, a feature, a publication item, an applicant etc)?

There are two ways to remove an object. You can right-click it, and then select Delete 'object' from the pop-up menu. Alternatively, select an object and press the Delete key.

Note that in some cases the delete operation is disabled. This happens when there is a biological reason for not allowing an object to be deleted until another object is removed.

I cannot delete a feature. Why not?

The delete operation is disabled in some cases. This happens when there is a biological reason for not allowing an object to be deleted until another object is removed.

You cannot delete:

a sequence that has been generated from a CDS feature until this CDS feature or the sequence to which it belongs is deleted.
a "source" feature, if there is only one.

How do I edit an object (ie, a sequence, a feature, a publication item, an applicant etc)?

Right-click the object, and then select Edit 'object' from the pop-up menu. The editor for this object will open. After editing, press the Save button or Control-S to save your changes.

Some objects are not editable. Why is this?

You cannot edit a generated protein sequence or its annotations (features) wherever these have been taken from the original nucleotide sequence. However, you can edit annotations added to such a sequence after its generation.

Which languages are supported?

The languages currently supported are:

English
French
German

Is it possible to have other language versions?

Yes, but the EPO can support only those language versions indicated above.
If you need a version in a language that is not on the supported list, please contact bissap@epo.org.

Can BiSSAP be installed in server-client mode?

No. BiSSAP is standalone desktop application and there is no option for having it in server-client mode.

Verification

What is verification in BiSSAP?

There are two kinds of verification in BiSSAP:

form validation - performed on every form, making it impossible to save a form containing incorrect data.
project verification - performed on a project at your request, or automatically after the sequence listing has been loaded or during output file generation just before writing to disk.

more about BiSSAP verification

What kind of rules exist for form validation?

It generally depends on the form. BiSSAP always checks whether all required fields contain a value. It also checks certain fields to see whether they contain allowed values.

In the case of features and qualifiers, BiSSAP checks whether the qualifiers are allowed for a given feature. There is also a check to see if all the required qualifiers have been put into the qualifiers list. Some qualifiers are checked to see whether they are in the correct format (for further information see http://www.ebi.ac.uk/embl/WebFeat/index.html )
In the case of sequences, BiSSAP checks the correctness of the symbols depending on the sequence type. Wrong characters are eliminated.

Why are some rules repeated in the verification if it is impossible to save a form with incorrect data?

Errors may be introduced during import. BiSSAP has to allow you to import wrong data so that you can modify it and then generate the correct file.

How reliable is the BiSSAP verification?

Experience shows that applicants submit surprisingly many files containing simple errors. These are errors that can be eliminated.

The set of rules is not complete, so there is no guarantee that a positively verified file will be accepted. The final decision always lies with the curators who get the file after automatic verification.

This is particularly true of the Organism field. The suggestions are more numerous than the values allowed in the sequence submission. The rule of thumb is that the scientific Latin names will be accepted. The rest may or may not be accepted, depending on the rules applicable in the particular case.

more about BiSSAP verification

Applicants

How are applicants managed in BiSSAP?

There is an internal database, which contains the information on applicants. If you want to add an applicant to a project, you can create one from scratch or assign an applicant already existing in the database. These actions are called Create Applicant and Add Applicant, respectively. If you decide to create a new applicant, a form will appear into which you can enter the applicant data.

What is an address book?

In the XML format, a single applicant field contains one or more address books (contacts). Each address book in turn contains data on a given applicant. BiSSAP uses a similar structure for applicants. For further details, please consult the information on ST.36.

Why is the applicant field so complicated?

The applicant field requires the same data required under the ST.36 patent standard. However, you do not have to fill in all the fields. The required fields are marked with a red triangle.

What if the same applicant is imported twice?

If the same applicant is imported twice, it will be stored in the applicant database twice, i.e. there is no unique logical identifier for the applicants. Implementing a sophisticated system to recognise which applicant is which in every case is not justified by the size of the BiSSAP user base. Consequently there may be several applicant objects in the database, each referring to the same person or organisation.

What should I know about importing an applicant into an ST.25 file?

BiSSAP remembers applicants in its database, which reflects the structure of the proposed new XML sequence listing standard. This structure differs from the ST.25 format, which uses only one unstructured text field. There is no restriction on what this field can contain. BiSSAP tries to parse this field when the sequence listing is loaded from an ST.25 file, and asks you which type of applicant it is.

In such cases not all elements of the applicant structure can be filled in. BiSSAP accepts the applicant, but you will have to add the missing information if you subsequently edit that applicant.

What should I know about exporting an applicant into an ST.25 file?

When an applicant is exported to the ST.25 format, the following occurs:

if the address book contains only text, the field is exported as a <110> field
if the address book contains structured data, that data goes on to be generated in a single field

Even if you want to generate ST.25 files only, you must provide fully structured applicant information. Reformatting as a single unformatted field does not take place until the output-file generation process.

Examples of exports of the same information in the ST.25 and XML formats

The applicant in the ST.25 file is imported as a text field. The applicant name is not parsed in such a way that it can be entered correctly in the full XML field. However, applicants imported from XML files can still be exported correctly into ST.25 files.

Can I edit applicants in ST.25 files?

No, but you can create another applicant and enter into it the desired new data. If you do not do this, the applicant will still be exported into the XML format, but not into the structured field.

The recommendation is to use the normal applicant fields. They will still be generated correctly when exporting into the ST.25 format.

What is the applicant tool?

The applicants are remembered in the application for reuse in sequence listings. If you add an applicant, it always remains in the applicant database. You can then reuse such applicants in later applications.

However, there is no control of duplicates. That means that if you create another applicant with the same name, it will be in the database twice.

Sequences

Can I copy a sequence?

Yes. see instructions.

How can I enter some additional description to a sequence?

If you are just creating the sequence (you are using Create sequence window): enter the information in the Additional sequence description field (max. 260 characters).
If the sequence has been already created: see instructions.

How can I enter amino acids in 3-letter code?

Once you set the Molecule type to PRT in the Create sequence window or in the sequence editor, the button Insert 3-letter code is enabled. Click on it, enter your sequence in 3-letter code in the window which pops-up and clik on Transform button.

Can I save a partially valid sequence?

Yes and no. You cannot save a sequence containing information that is plainly wrong, like incorrect nucleotide symbols. However, some bibliographical information is verified only when you choose Verify Project, or when the output file is generated.

Features

How can I express the location of a feature?

There are several ways of describing the location depending on the feature, for example: a simple point, sequence span, partial region, between locations etc. For an overview of the feature location formats - see Feature locations chapter.

Can I copy a feature?

Yes. see instructions.

Can I save a partially valid feature?

No.