Subgraph Queries by Context-free Grammars
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doi:10.2390/biecoll-jib-2008-100
June 19, 2008
August 25, 2008
PubMed ID 20134073
Petteri Sevon and Lauri Eronen
Correspondence should be addressed to:
Lauri Eronen
Helsinki Institute for Information Technology, Department of Computer Science,PO Box 68, FI-00014 University of Helsinki, Finland
if.iknisleh.sc@nullnenore.irual
Abstract
We describe a method for querying vertex- and edge-labeled graphs using context-free grammars to specify the class of interesting paths. We introduce a novel problem, finding the connection subgraph induced by the set of matching paths between given two vertices or two sets of vertices. Such a subgraph provides a concise summary of the relationship between the vertices. We also present novel algorithms for parsing subgraphs directly without enumerating all the individual paths. We evaluate experimentally the presented parsing algorithms on a set of real graphs derived from publicly available biomedical databases and on randomly generated graphs. The results indicate that parsing the connection subgraph directly is much more effective than parsing individual paths separately. Furthermore, we show that using a bidirectional parsing algorithm, in most cases, allows for searching twice as long paths as using a unidirectional search strategy.