A2-D3 summarizes the use cases and tools developed by various A2 members, which have
the potential to integrate REWERSE technologies. The described use cases cover a wide range
of bioinformatics tasks that are representative examples of the kinds of problems addressed in
real bioinformatics applications. These use cases have been selected also to be advanced and
challenging, and illustrating the need for Semantic Web technology. The use cases should not
be seen as separate stand-alone example applications, but rather as parts of a larger scenario,
where a researcher applies a number of different bioinformatics tools for investigating different
aspects of a particular biological system. A description of an overall sample application is
provided at the end of this document.
Before we introduce the use cases in detail, let us summaries them according to their maturity,
and the web and rule technologies, which are needed to realize the use cases. All of the
proposed use cases are extending existing deployed or research prototypes and sketch opportunities
for web/rule technologies. The scope of the systems ranges from basic research to fully
deployed systems with many real users world-wide. Most of the proposed use cases can be directly
linked to I4 and I5 technologies in that they require some form of querying and sometimes
reactive behavior. Some of the use cases refer already directly to technologies investigated in
workpackages I4 and I5, namely Prova (I5), Xcerpt (I4), and Erus (I5). Common to many use
cases is the need to work with web services, ontologies, databases, and XML documents.
Defines standard
Replaced/Superseded by document(s)
Cancelled by
Amended by
| File | MIME type | Size (KB) | Language | Download | |
|---|---|---|---|---|---|
| Example RE Bioinformatics Use Cases a2-d3.pdf | application/pdf | 1.36 MB | English | DOWNLOAD! |
Provides definitions
Cover images
Introduction
This deliverable specifies use cases based on bioinformatics research carried out by members of
A2. The use cases involve the use of rules to reason over ontologies and pathways (Dresden,
Edinburgh, Paris, Link¨oping) and rules to specify workflows to integrate bioinformatics data
(Lisbon, Sk¨ovde, Jena, Bucharest). The use cases are designed as a reference point to foster
the take up of A2 use cases by I-workpackages. Most notably, many of the use cases specify the
need for querying and reactivity with languages like Xcerpt (I4), Erus (I5) and Prova (I5). The
use cases range from basic research applications to fully deployed software with an international
user base.