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Table 4 Comparison of search results by two search methods.

From: An ontology-based search engine for protein-protein interactions

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%)
  1. 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.