Table 5.
Example of an article containing multiple gene and specie mentions (PMC2680910)
| PMCID2680910 | Central Vote | Curated Outputa | System Raw Output Team | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene ID | Gene names | Species | 1 | 2 | 3 | 4 | 5 | 78 | 68 | 65 | 93 | 89 | |
| 10015 | ALIX | human | 7 | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C |
| 57630 | POSH | human | 7 | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C | Y, C |
| 155030 | Gag | HIV-1 | 6 | Y, C | Y, C | - | Y, C | Y, C | Y, C | - | - | Y, C | - |
| 36990 | POSH | Drosophila | Y | Y | Y | Y | Y | Y | Y | - | Y | Y | |
| 43330 | ALIX | Drosophila | Y | Y | Y | Y | Y | Y | Y | - | - | Y | |
| 128866 | CHMP4B | human | Y | Y | Y | Y | - | Y | - | Y | - | Y | |
| 39659 | TAK-1 | Drosophila | Y | Y | Y | Y | Y | - | Y | - | - | Y | |
| 3355106 | ALG-2 | Drosophila | Y | Y | Y | Y | Y | - | - | - | Y | - | |
| 7323 | UbcH5c | human | Y | Y | Y | Y | - | - | Y | Y | - | - | |
| 1489984 | p9 | EIAV | Y | Y | Y | Y | - | - | - | - | - | - | |
| 137492 | HCRP1 | human | Y | Y | Y | Y | - | Y | - | Y | - | - | |
| 7251 | TSG101 | human | Y | Y | Y | Y | - | Y | - | Y | - | - | |
| 155030 | p6 | HIV-1 | Y | - | Y | Y | - | - | - | - | - | - | |
| 7334 | UBC13 | human | 1 | Y | - | Y, C | Y | - | Y | Y | Y | - | - |
| Total genes detected | 14 | 19 | 13 | 26 | 10 | 90 | 22 | 120 | 9 | 52 | |||
| FP | 0 | 5 | 0 | 0 | 3 | 81 | 15 | 113 | 4 | 46 | |||
| FN | 0 | 2 | 1 | 0 | 7 | 5 | 7 | 7 | 8 | 8 | |||
| TP | 14 | 12 | 13 | 14 | 7 | 9 | 7 | 7 | 5 | 6 | |||
| Precision | 1.00 | 0.71 | 1.00 | 1.00 | 0.70 | 0.10 | 0.32 | 0.06 | 0.56 | 0.12 | |||
| Recall | 1.00 | 0.86 | 0.93 | 1.00 | 0.50 | 0.64 | 0.50 | 0.50 | 0.38 | 0.43 | |||
List of Entrez Gene ID, gene name and species found in PMC2680910. 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 manual curation (2 curators, 1-2) and system-assisted curation (5 curators, but 3 are shown, 3-5).