A query language for biological networks.
BACKGROUND
Many areas of modern biology are concerned with the management, storage, visualization, comparison and analysis of networks, but no appropriate query language for such complex data structures yet exists.


RESULTS
We have designed and implemented the pathway query language (PQL) for querying large protein interaction or pathway databases. PQL is based on a simple graph data model with extensions reflecting properties of biological objects. Queries match subgraphs in the database based on node properties and paths between nodes. The syntax is easy to learn for anybody familiar with SQL. As an important feature, a query may require a certain structure in the database to exist but return a different subgraph. We have tested PQL queries on networks of up to 16,000 nodes and found it to scale very well.


BACKGROUND
The code is available on request from the author.
Leser
Ulf
U
Department for Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany. leser@informatik.hu-berlin.de
D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D018511:Systems Integration; D014584:User-Computer Interface
D020543:Proteome