Concepts

This page describes the key concepts in BiSSAP.

BiSSAP is primarily a tool for applicants. It is designed to raise the overall quality of sequence listings submitted to patent offices. Better quality should, in turn, simplify and streamline the work of applicants and patent offices alike.

You can use BiSSAP to perform two main tasks:

• prepare sequence listings for submission to patent offices
• verify data before it is sent.

The verification engine used by patent offices is/will be essentially the same as the one in BiSSAP, which means that you can use this application to check your files using the same tool that patent offices use.

Projects and sequence listings

At the heart of BiSSAP is an internal database, which contains all the information on projects, sequences, features, etc.

All work in BiSSAP centres around a project. A project is a set of general and biological data that is used to generate a single sequence listing file. Each project in BiSSAP has a unique name (an application-specific requirement). This differs from the invention title, which is the text written to the sequence listing file. Changes to the name of the project have no bearing on the generated sequence listing.

Before the sequence listing is generated, the temporary data is kept in the internal database. Individual data elements like sequence, feature and applicant are created, modified and saved independently of each other, i.e. there is no need to save the entire project.

Project data is kept in the BiSSAP workspace until the project is removed from the database. The data can be modified as required. You can stop working on the project at almost any time, and then resume again without data loss.

Please note that you cannot copy BiSSAP files to another location because BiSSAP is a database system and no such files exist. To copy data, please use the appropriate BiSSAP feature, i.e. importing and exporting drafts or the backup and restore mechanism.

Enabling you to focus on your data

BiSSAP supports many file types. However, the file-type information appears only at the import and export stages. This means that when you are using BiSSAP, you can focus on your data: applicants, priority claims, application references, sequences, features, etc. You do not have to bother about the format until the export stage.

BiSSAP does not provide an editor for particular file types but rather for particular data elements like sequences, features, applicants, etc.

The architecture of BiSSAP can be extended to cater for special file formats not yet implemented.

When you have finished work on the sequence listing, export it into one of the approved formats. Just before export, the data is verified once again and a list of errors is displayed. If there are serious errors, the export is not performed.

Typical workflow

New submissions (sequence listings from scratch)

1. Create the project in BiSSAP
2. Add and edit sequences and features to the project
3. Add, edit and remove applicants
4. Verify
5. Export (generate) the files into ST.25 or XML formats.

For patent applications, ST.25 (or XML in the future) is the mandatory format. Only if you are submitting files to institutions like EBI should you export your sequence listings into EMBL format.

Existing files

When working with existing files, the typical workflow looks like this:

1. Import an ST.25 or XML file
2. Edit the project, i.e. add/edit/remove sequences, features and the general part
3. Add, edit and remove applicants
4. Verify
5. Export (generate) the files into ST.25 or XML formats.

Importing and exporting drafts

You can transfer drafts between BiSSAP installations by using the importing and exporting drafts mechanism.

Batch verification

You can also perform batch verification on a group of files.

Workbench

Workbench is where you interact with the program. Editors, viewers and browsers can be freely arranged within the main workbench window (the main window of BiSSAP). This way you can adapt the program to your needs, style of work, monitor size, etc.

You can also change other settings, like the colour of window headers, via Preferences. However, it is recommended that you leave the default settings for a "look and feel" that is consistent throughout the application.

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Language support

BiSSAP is available in English (status June 2011) and will become available in a limited number of other languages. It can, however, potentially support any language.

The only part of the interface that will not be localised into other languages is the log messages. These are intended for the developers who maintain the application. Translation could change the structure of these messages and cause technical problems.