TY - GEN
T1 - Enhancing graph database indexing by suffix tree structure
AU - Bonnici, Vincenzo
AU - Ferro, Alfredo
AU - Giugno, Rosalba
AU - Pulvirenti, Alfredo
AU - Shasha, Dennis
PY - 2010
Y1 - 2010
N2 - Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model such kinds of data. To fully exploit the wealth of information in these graph databases, scientists require systems that search for all occurrences of a query graph. To deal efficiently with graph searching, advanced methods for indexing, representation and matching of graphs have been proposed. This paper presents GraphGrepSX. The system implements efficient graph searching algorithms together with an advanced filtering technique. GraphGrepSX is compared with SING, GraphFind, CTree and GCoding. Experiments show that GraphGrepSX outperforms the compared systems on a very large collection of molecular data. In particular, it reduces the size and the time for the construction of large database index and outperforms the most popular systems.
AB - Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model such kinds of data. To fully exploit the wealth of information in these graph databases, scientists require systems that search for all occurrences of a query graph. To deal efficiently with graph searching, advanced methods for indexing, representation and matching of graphs have been proposed. This paper presents GraphGrepSX. The system implements efficient graph searching algorithms together with an advanced filtering technique. GraphGrepSX is compared with SING, GraphFind, CTree and GCoding. Experiments show that GraphGrepSX outperforms the compared systems on a very large collection of molecular data. In particular, it reduces the size and the time for the construction of large database index and outperforms the most popular systems.
KW - graph database search
KW - indexing
KW - molecular database
KW - subgraph isomorphism
KW - suffix tree
UR - http://www.scopus.com/inward/record.url?scp=78049453458&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=78049453458&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-16001-1_17
DO - 10.1007/978-3-642-16001-1_17
M3 - Conference contribution
AN - SCOPUS:78049453458
SN - 364216000X
SN - 9783642160004
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 195
EP - 203
BT - Pattern Recognition in Bioinformatics - 5th IAPR International Conference, PRIB 2010, Proceedings
T2 - 5th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2010
Y2 - 22 September 2010 through 24 September 2010
ER -