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Table 2 Final network extraction system evaluation metrics

From: Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

Source (1) (2) (3) (4) (5) (6) (7) (8) (9)
RegulonDB (as of June 2006) 3108 - 3397 3397 100% 100% - - -
AS 3148 768 661 1429 45% 45% 0.45 0.77 0.57
AS* 2649 569 535 1104 41% 35.5% 0.41 0.72 0.47
RP 2650 711 605 1316 49% 42% 0.49 0.78 0.55
RP* 2202 522 491 1013 46% 32% 0.46 0.74 0.45
RN 1643 555 471 1026 62% 33% 0.62 0.85 0.47
RN* 1354 426 385 811 59% 26% 0.59 0.81 0.39
EA 627 262 140 402 64% 12% 0.64 0.95 0.22
EA* 554 217 114 331 59% 10% 0.59 0.91 0.19
RS 718 254 146 400 55% 12% 0.55 0.91 0.22
RS* 630 207 121 328 52% 10% 0.52 0.86 0.18
ST 691 199 143 342 49% 11% 0.49 0.90 0.19
ST* 628 170 118 288 45% 9% 0.45 0.86 0.16
RA 414 207 115 322 77% 10% 0.77 1.00 0.18
RA* 370 180 97 277 74% 8% 0.74 0.99 0.16
  1. An asterisk [*] next to source name indicates that no multiple-unit objects (like the individual elements of two-system components, or operons) were added; The RegulonDB "dual" interactions (that is, presenting both activation and repression), are counted here as two distinct interactions. AS represents a file containing all compiled interactions found in all textual sources used in this work, and constitutes the sum of all non-redundant interactions extracted from the full-text and abstract documents.
  2. 1. Unique, non-repeated interactions found for each file
  3. 2. Interactions that match RegulonDB interaction pairs, but whose function (activation or repression) was not determined by the system.
  4. 3. Interactions that match RegulonDB entries, and also match repressor/activator function
  5. 4. Overall matches (column 2 + column 3), including both interactions with complete information as well as under specified ones
  6. 5. % of total interactions in file which are correct: (1)/(4)
  7. 6. Recall: percentage of RegulonDB's 3108 interactions that is represented by correct interactions in file: ((4)*100)/3108
  8. 7. Precision 1: Number of overall matches (4)/unique interactions in file (1)
  9. 8. Precision 2: Number of overall matches (4)/interactions in file that contain a RegulonDB-annotated regulator
  10. 9. F-Measure (F = 2RP/R+P)