Table 2:
Query Results for the Different Experiments
| Scope | DB | Drug Phase | FDA/CT, NCI | Source | Freq. | Predicates | Drug ST | Doc. | Drug | Recall | Prec. | F1 | F2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Experiment 1: Preliminary 1 Gene Sheet, 7 reference drugs | SemMedDB_Local | Mixed | Yes | Pred. | >2 | INHIBITS, INTERACTS_WITH | phsu, antb | 559 | 74 | 1.0 | 0.09 | 0.17 | 0.33 |
| SemMedDB | Mixed | Yes | Pred. | >2 | INHIBITS, INTERACTS_WITH | phsu, antb | 540 | 35 | 0.29 | 0.06 | 0.1 | 0.16 | |
| Experiment 2: Parameter Selection 4 Gene Sheets, 115 reference drugs | SemMedDB_UTH | Marketed | Yes | Pred. | >4 | INHIBITS, INTERACTS_WITH, COEXISTS_WITH | phsu, orch | 624 | 50 | 0.86 | 0.12 | 0.21 | 0.39 |
| 3 | Yes | Pred. | – | INHIBITS, INTERACTS_WITH, COEXISTS_WITH | – | 242 | 42 | 0.79 | 0.26 | 0.39 | 0.56 | ||
| 2 | Yes | CoOccSen | – | – | – | 1466 | 125 | 0.69 | 0.18 | 0.29 | 0.44 | ||
| 1/2 | Yes | CoOccSen | – | – | – | 993 | 25 | 0.45 | 0.20 | 0.28 | 0.36 | ||
| 1 | Yes | CoOccDoc | – | – | – | 544 | 99 | 0.39 | 0.20 | 0.26 | 0.33 | ||
| All Phases: | 3869 | 341 | 0.56 | 0.19 | 0.28 | 0.4 | |||||||
| Experiment 3: Evaluation 17 Gene Sheets, 276 reference drugs | SemMedDB_UTH | Marketed | Yes | Pred. | >4 | INHIBITS, INTERACTS_WITH, COEXISTS_WITH | phsu, orch | 2251 | 80 | 0.69 | 0.3 | 0.42 | 0.55 |
| 3 | Yes | Pred. | – | INHIBITS, INTERACTS_WITH, COEXISTS_WITH | – | 299 | 61 | 0.35 | 0.3 | 0.32 | 0.34 | ||
| 2 | Yes | CoOccSen | – | – | – | 4723 | 205 | 0.5 | 0.17 | 0.25 | 0.36 | ||
| 1/2 | Yes | CoOccSen | – | – | – | 3875 | 40 | 0.29 | 0.18 | 0.22 | 0.26 | ||
| 1 | Yes | CoOccDoc | – | – | – | 1609 | 129 | 0.25 | 0.19 | 0.22 | 0.24 | ||
| All Phases: | 12757 | 515 | 0.39 | 0.21 | 0.27 | 0.33 | |||||||
| SemMedDB | Marketed | No | Pred. | – | INHIBITS, INTERACTS_WITH, COEXISTS_WITH | phsu, orch | 1730 | 661 | 0.46 | 0.02 | 0.04 | 0.09 | |
| 3 | No | Pred. | – | INHIBITS, INTERACTS_WITH, COEXISTS_WITH | phsu, orch | 1730 | 661 | 0.17 | 0.01 | 0.02 | 0.04 | ||
| 2 | No | Pred. | – | INHIBITS, INTERACTS_WITH, COEXISTS_WITH | phsu, orch | 1730 | 661 | 0.1 | 0.01 | 0.02 | 0.04 | ||
| 1/2 | No | Pred. | – | INHIBITS, INTERACTS_WITH, COEXISTS_WITH | phsu, orch | 1730 | 661 | 0.04 | 0.002 | 0.004 | 0.01 | ||
| 1 | No | Pred. | – | INHIBITS, INTERACTS_WITH, COEXISTS_WITH | phsu, orch | 1730 | 661 | 0.01 | 0.002 | 0.003 | 0.01 | ||
| All Phases: | 1730 | 661 | 0.12 | 0.05 | 0.07 | 0.09 | |||||||
FDA, Food and Drug Administration; NCI, National Cancer Institute. DB, Database used to run the queries; FDA/CT, NCI, Filters used to refine the results; Freq., Frequency filter; Drug ST, Drug semantic type (antb, ; orch, organic chemical; phsu, pharmaceutical substance); Doc., Number of documents returned; Drug, Number of concepts returned by the query; Prec., Precision; F1, Harmonic mean; F2, A variant of F1, emphasizing recall.