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Table 6 Example of an article where a new gene name is introduced (PMC2764847).

From: BioCreative III interactive task: an overview

PMC2764847

 

Central Vote

Curated Outputa

System Raw Output Team

Gene ID

Gene name

Species

  

78

68

65

93

89

828316

AtIscU1

A. thaliana

9

Y, C

-

-

-

-

-

829947

AtHscA1

A. thaliana

8

Y, C

-

-

-

-

-

830529

AtHscB

A. thaliana

8

Y, C

-

Y

-

Y, C

-

852866

Jac1

Yeast

8

Y, C

Y, C

Y, C

Y, C

-

Y, C

851084

Ssq1

Yeast

8

Y, C

Y, C

Y, C

Y, C

-

Y, C

830818

HscA2

A. thaliana

1

Y

-

-

-

-

-

821316

AtIscU2

A. thaliana

1

Y

-

-

-

-

-

825719

AtIscU3

A. thaliana

1

Y

-

-

-

-

-

 

Total genes detected

29 (manual)

54

22

65

9

23

  

FP

  

46

14

58

7

16

  

FN

  

21

21

19

27

22

  

TP

  

8

8

10

2

7

  

Precision

0.93 (0.07)b

0.15

0.36

0.15

0.22

0.30

  

Recall

0.75 (0.16)b

0.28

0.28

0.34

0.07

0.24

  1. There were a total of 29 gene mentions in the article (as determined independently by manual curation), but for simplicity, only the list of proposed central genes are listed here (as considered by 10 curators). The Central Vote column indicates the number of curators that selected the gene as central; “Y”: gene mentioned in the article is detected; “-”:gene mentioned was missed; “C”=indicates central gene as determined by majority vote, and in the systems it means that the gene was ranked high by the system (gene ranked higher than non central genes); “Total genes detected”: totality of gene mentions provided by a given system (what the system considered a gene). FP and FN stand for false positive and negative, respectively. aCurated output by 10 curators (2 per system). Central genes were selected by majority vote, with previous revision of discrepancies of annotation with individual UAG members. bAverage value from curators output with standard deviation shown in parenthesis.