Table 9.

Performance analysis via incorporation of gold standard in different steps

	Analysis method	F1 (exact, Task 1) (%)	F1 (relaxed, Task 1) (%)	F1 (exact, Task 2) (%)	F1 (hierarchy, Task 2) (%)
1	Baseline, Result 11 in Table 3 (Subtask 1), Result 5 in Table 6 (Subtask 2)	22.1	35.7	10.6	21.4
2	Add the gold standard evidence sentences to the gene sentences to be classified	31.8	46.2	12.5	24.9
3	Based on Result 2, replace all the gene IDs by the same ID for Subtask1	36	53.4	12.5	24.9
4	Use the gold standard of Subtask 1 as the input of Subtask 2	100	100	19.6	33.1
5	Replace the final result by the gold standard of Subtask 2 only for the terms with the frequency over 2000 in GO annotation databases	100	100	61.2	65.4