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Bioinformatics. 2005 Sep 1;21 Suppl 2:ii33-9.

A query language for biological networks.

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  • 1Department for Computer Science, Humboldt-Universit├Ąt zu Berlin, Berlin, Germany.



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.


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.


The code is available on request from the author.

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