From: Primmer et al. 2013 Annotated genes and non-annotated genomes: cross-species use of Gene Ontology in ecology and evolution research
Table S1- Gene ontology evidence codes and their frequency (as of 1.2.2013) in some ‘traditional model’ and ‘emerging genomic model’
organisms.
Evidence code (abbreviation)1
Gene Ontology annotation number (% of species total)
Human
Arabadopsis Drosophila Chicken Zebrafinch Zebrafish 3 spine
Dog
Rice
stickleback
Experimental evidence (EXP)
24%
29%
43%
1%
0%
11%
0%
<1%
1%
Inferred from direct assay (IDA)
49523 31019
(14%) (17%)
11326
(14%)
430
0
(<1%) (0%)
2414
(2%)
0
(0%)
120
(<1%)
117
(<1%)
Inferred from physical interaction (IPI)
26488 6222
(7%) (3%)
2100
(3%)
204
0
(<1%) (0%)
511
(0%)
0
(0%)
15
(<1%)
6
(<1%)
Inferred from mutant phenotype (IMP)
9440
(3%)
18038
(22%)
146
0
(<1%) (0%)
7975
(6%)
0
(0%)
21
(<1%)
151
(<1%)
Inferred from generic interaction (IGI)
537
2545
(<1%) (1%)
2321
(3%)
6
0
(<1%) (0%)
2326
(2%)
0
(0%)
2
(<1%)
42
(<1%)
Inferred from expression pattern (IEP)
846
4194
(<1%) (2%)
952
(1%)
137
0
(<1%) (0%)
116
(<1%)
0
(0%)
1
(<1%)
65
(<1%)
10081
(5%)
Curated non-experimental annotations
27%
39%
41%
6%
<1%
5%
0%
4%
99%
19
(<1%)
3549
(3%)
0
(0%)
3388
(4%)
373
(1%)
Inferred from sequence of structural similarity (ISS)2
13853 25552
(4%) (14%)
15776
(19%)
3534
(4%)
Inferred from reviewed computational analysis (RCA)
42
37534
(<1%) (20%)
19
(<1%)
6
0
(<1%) (0%)
0
(0%)
0
(0%)
0
(0%)
46567
(94%)
Non-traceable author statement (NAS)
8732
(2%)
10588
(13%)
54
0
(<1%) (0%)
130
(<1%)
0
(0%)
16
(<1%)
0
(0%)
Traceable author statement (TAS)
68616 6058
(19%) (3%)
4846
(6%)
743
(1%)
0
(0%)
0
(0%)
21
(<1%)
13
(<1%)
Inferred by curator (IC)
1140 210
(<1%) (<1%)
1007
(1%)
11
0
(<1%) (0%)
83
(<1%)
0
(0%)
1
(<1%)
1962
(4%)
Other3
3145
(1%)
62
(<1%)
822
(1%)
0
(0%)
2833
(2%)
0
(0%)
165
(<1%)
0
(0%)
175341 59655
(49%) (32%)
14317
(18%)
83640
(93%)
112410
(100%)
104050 68441
(84%) (100%)
77606
(95%)
0
(0%)
357703 81356
81352
89733
112429
123987 68441
81356
49296
749
(<1%)
1081
(1%)
0
(0%)
Automatically assigned annotations
Inferred from electronic annotation (IEA)
Total GO annotations
1- Data taken from http://www.geneontology.org/GO.downloads.annotations.shtml for all species except zebrafinch and zebrafish, for which
data were extracted from http://www.ensembl.org/biomart/martview/
2- Includes the codes: Inferred from sequence orthology (ISO); Inferred from sequence alignment (ISA); Inferred from sequence model (ISM).
3- Includes the codes: Inferred from genomic content (IGC); Inferred from biological aspect of ancestor (IBA); Inferred from biological aspect
of descendant (IBD); Inferred from key residues (IKR); Inferred from rapid divergence (IRD).