An ontology-based search engine for protein-protein interactions

BMC Bioinformatics

Table 4 Comparison of search results by two search methods.

GO term ID	GO term name	ID-matching search	Ontology-based search
Biological process
GO:0008150	biological process	5 (0.01%)	36, 523 (95.63%)
GO:0008152	metabolic process	2, 862 (7.49%)	19, 828 (51.92%)
GO:0044238	primary metabolic process	0 (0.00%)	17, 434 (45.65%)
GO:0043170	macromolecule metabolic process	0 (0.00%)	7, 211 (18.88%)
GO:0019538	protein metabolic process	5, 324 (13.94%)	5, 659 (14.82%)
Molecular function
GO:0003676	nucleic acid binding	10 (0.03%)	8, 733 (22.87%)
GO:0003677	DNA binding	1, 944 (5.09%)	6, 935 (18.16%)
GO:0003700	transcription factor activity	5, 164 (13.52%)	5, 164 (13.52%)
Cellular component
GO:0005622	intracellular	0 (0.00%)	31, 694 (82.99%)
GO:0005737	cytoplasm	17, 312 (45.33%)	20, 990 (54.96%)
GO:0005829	cytosol	452 (1.18%)	452 (1.18%)

The number of protein-protein interactions found in HPRD release 7 by each search method. The numbers inside parentheses indicate the ratio of the interactions to the total 38, 190 interactions of HPRD. The ID-matching search often finds more interactions with a specialized GO terms than with a less specialized terms since it does not consider semantic relation between ontology terms.

ISSN: 1471-2105