GO2PUB: Querying PubMed with semantic expansion of gene ontology terms

Table 4 Measures for seven generalization queries

(A) Lipids	GO:0044242		GO:0008299		GO:0008654
Tool	GPM	G2P	GPM	G2P	GPM	G2P
(a) Number of results	4	26	9	16	25	27
(b) Relevant among (a)	3	20	1	2	5	11
(c) Total relevant	22		3		12
(d) Common results	1		2		5
(e) Relevant among (d)	1		0		4
Precision	0.750	0.769	0.111	0.125	0.200	0.407
Relative Recall	0.136	0.864	0.333	0.667	0.417	0.917
F-score	0.231	0.814	0.167	0.211	0.270	0.564
(B) Other	GO:0050658		GO:0033013		GO:0006805		GO:0048284
Tool	GPM	G2P	GPM	G2P	GPM	G2P	GPM	G2P
(a) Number of results	25	10	15	19	30	23	24	17
(b) Relevant among (a)	7	2	3	3	17	14	10	9
(c) Total relevant	9		6		26		16
(d) Common results	3		6		7		8
(e) Relevant among (d)	1		2		4		4
Precision	0.280	0.200	0.200	0.158	0.567	0.609	0.417	0.529
Relative Recall	0.875	0.250	0.600	0.600	0.680	0.560	0.625	0.563
F-score	0.424	0.222	0.300	0.250	0.618	0.583	0.500	0.545

Results’ sets sizes and values of precision, relative recall and F-score using GoPubMed and GO2PUB search tools for seven random queries: three lipid-related queries (part A) and four queries about other topics (part B). Values of precision, relative recall and F-score are calculated from (a), (b) and (c) lines. (d) and (e) lines provide GO2PUB and GoPubMed common results’ sets sizes and the number of common relevant results.

ISSN: 2041-1480