Where patent applications refer to biological sequences (like DNA or proteins), these sequences need to be disclosed by applicants. The files that applicants submit have to meet a certain standard so that all parties concerned - the applicants themselves, patent offices and, later, others - have a common understanding of the invention. There are a number of different standards for defining a sequence, or a "sequence listing" (the way we refer to a given set of sequences).
The format currently used in the patent world is the World Intellectual Property Organization (WIPO) Standard ST.25. This is a text format designed to be both human- and computer-readable. In ST.25 files, the fields are lines that begin with a specific numeric code [ http://www.wipo.int/standards/en/pdf/03-25-01.pdf ].
What happens next varies from office to office, but some steps are common to all: when it receives the data, the patent office (e.g. the EPO) conducts manual and computerised verification procedures. If the files are in order, they are prepared for substantive examination. They are also stored (in a database) for future publication.
When examiners decide to grant a patent, the sequence listing is usually published in electronic form. Sequence listings are usually accessible via the facilities provided by public database providers like the European Bioinformatics Institute (EBI), the National Center for Biotechnology Information (NCBI) or the DNA Data Bank of Japan (DDBJ). For legal reasons, they are published separately by WIPO and/or the patent office.
If files are incorrect, the patent office and the applicant can take steps to correct them. Or, better still, applicants can verify the sequence listing before it is submitted. This is where a verification tool comes in.
At the end of the year 2010, WIPO set up a task force to create a new standard based on XML. When the new standard is approved, an editor (popularly called a submission tool) will be needed.
Biological Sequence Submission Application for Patents, or BiSSAP for short, is a multilingual desktop application, which the EPO in co-operation with EBI has decided to develop to handle the proposed new standard for sequence presentation and the extensive verification of sequence listings.
BiSSAP prepares sequence listing files in various formats, and verifies their content. The tool will be freely available to applicants and patent offices.
Help documentation
This help documentation describes BiSSAP and how to use it, and provides some information on sequence listings. It is a set of HTML pages accessible within the application as context-sensitive help. You can also read it chapter-by-chapter, in a conventional manner, via a browser (like Firefox or Internet Explorer).
The help is divided into the following sections:
Getting started
An overview of how BiSSAP works, its philosophy and an installation guide. Tutorial on performing the most common operations.
Description of sequence listings
This is a description of the file formats you can use with BiSSAP. It also contains references to web resources about the different formats in existence.
Reference
Detailed description of various BiSSAP elements, GUIs, file formats, fields, features, qualifiers, etc.
Frequently asked questions
This is where you will find answers to some of the questions you may have. If the question you want to ask if not there, please send it to us by e-mail (bissap@epo.org). And who knows? Your question may even be included in the list of FAQs for future releases of BiSSAP.
Samples
Samples of documents generated by BiSSAP.
Licence and legal information
The BiSSAP licence and the legal obligations attached to using the software. Before using BiSSAP, you must read and accept in full this information.