Subgraph queries by context-free grammars

Petteri Sevon, Lauri Eronen
2008 Journal of Integrative Bioinformatics  
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
more » ... s. 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.
doi:10.2390/biecoll-jib-2008-100 pmid:20134073 fatcat:zepjqlq3pvgsdcdzizypfa5gbq