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Proceedings of the 2008 ACM SIGMOD international conference on Management of data
A query language for analyzing networks
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Advanced querying interface for biochemical network databases
Proceedings of the 2010 ACM Symposium on Applied Computing
GBLENDER: towards blending visual query formulation and query processing in graph databases
Proceedings of the 2010 ACM SIGMOD International Conference on Management of data
Analyzing graph databases by aggregate queries
Proceedings of the Eighth Workshop on Mining and Learning with Graphs
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
bcnQL: A query language for biochemical networks
International Journal of Data Mining and Bioinformatics
Proceedings of the thirtieth ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems
Query languages for graph databases
ACM SIGMOD Record
Regular path queries on graphs with data
Proceedings of the 15th International Conference on Database Theory
Regular path queries on large graphs
SSDBM'12 Proceedings of the 24th international conference on Scientific and Statistical Database Management
BiQL: a query language for analyzing information networks
Bisociative Knowledge Discovery
Expressive languages for selecting groups from graph-structured data
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Querying Regular Graph Patterns
Journal of the ACM (JACM)
Hybrid query execution engine for large attributed graphs
Information Systems
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Motivation: 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. Availability: The code is available on request from the author. Contact: leser@informatik.hu-berlin.de