BioNLP'09 Shared Task on
Event Extraction
in conjunction with
BioNLP, a NAACL-HLT 2009
workshop, June 4-5 2009, Boulder, Colorado
Final Evaluation Results
of Pathway and Interaction Knowledge Base
Task 1
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 19) 23 ( 19) 10.92 82.61 19.29
Binding 347 ( 25) 63 ( 25) 7.20 39.68 12.20
Gene_expression 722 ( 220) 295 ( 220) 30.47 74.58 43.26
Transcription 137 ( 15) 38 ( 15) 10.95 39.47 17.14
Protein_catabolism 14 ( 4) 7 ( 4) 28.57 57.14 38.10
Phosphorylation 135 ( 46) 53 ( 46) 34.07 86.79 48.94
==[EVT-TOTAL]== 1529 ( 329) 479 ( 329) 21.52 68.68 32.77
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Regulation 291 ( 4) 15 ( 4) 1.37 26.67 2.61
Positive_regulation 983 ( 11) 43 ( 11) 1.12 25.58 2.14
Negative_regulation 379 ( 1) 1 ( 1) 0.26 100.00 0.53
==[REG-TOTAL]== 1653 ( 16) 59 ( 16) 0.97 27.12 1.87
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==[ALL-TOTAL]== 3182 ( 345) 538 ( 345) 10.84 64.13 18.55
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 19) 23 ( 19) 10.92 82.61 19.29
Binding 347 ( 25) 63 ( 25) 7.20 39.68 12.20
Gene_expression 722 ( 225) 295 ( 225) 31.16 76.27 44.25
Transcription 137 ( 19) 38 ( 19) 13.87 50.00 21.71
Protein_catabolism 14 ( 4) 7 ( 4) 28.57 57.14 38.10
Phosphorylation 135 ( 48) 53 ( 48) 35.56 90.57 51.06
==[EVT-TOTAL]== 1529 ( 340) 479 ( 340) 22.24 70.98 33.86
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Regulation 291 ( 5) 15 ( 5) 1.72 33.33 3.27
Positive_regulation 983 ( 12) 43 ( 12) 1.22 27.91 2.34
Negative_regulation 379 ( 1) 1 ( 1) 0.26 100.00 0.53
==[REG-TOTAL]== 1653 ( 18) 59 ( 18) 1.09 30.51 2.10
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==[ALL-TOTAL]== 3182 ( 358) 538 ( 358) 11.25 66.54 19.25
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 19) 23 ( 19) 10.92 82.61 19.29
Binding 347 ( 25) 63 ( 25) 7.20 39.68 12.20
Gene_expression 722 ( 225) 295 ( 225) 31.16 76.27 44.25
Transcription 137 ( 19) 38 ( 19) 13.87 50.00 21.71
Protein_catabolism 14 ( 4) 7 ( 4) 28.57 57.14 38.10
Phosphorylation 135 ( 48) 53 ( 48) 35.56 90.57 51.06
==[EVT-TOTAL]== 1529 ( 340) 479 ( 340) 22.24 70.98 33.86
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Regulation 291 ( 5) 15 ( 5) 1.72 33.33 3.27
Positive_regulation 983 ( 12) 43 ( 12) 1.22 27.91 2.34
Negative_regulation 379 ( 1) 1 ( 1) 0.26 100.00 0.53
==[REG-TOTAL]== 1653 ( 18) 59 ( 18) 1.09 30.51 2.10
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==[ALL-TOTAL]== 3182 ( 358) 538 ( 358) 11.25 66.54 19.25
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 19) 23 ( 19) 10.92 82.61 19.29
Binding 398 ( 49) 77 ( 49) 12.31 63.64 20.63
Gene_expression 722 ( 220) 295 ( 220) 30.47 74.58 43.26
Transcription 137 ( 15) 38 ( 15) 10.95 39.47 17.14
Protein_catabolism 14 ( 4) 7 ( 4) 28.57 57.14 38.10
Phosphorylation 135 ( 46) 53 ( 46) 34.07 86.79 48.94
==[EVT-TOTAL]== 1580 ( 353) 493 ( 353) 22.34 71.60 34.06
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Regulation 338 ( 8) 15 ( 8) 2.37 53.33 4.53
Positive_regulation 1186 ( 14) 43 ( 14) 1.18 32.56 2.28
Negative_regulation 416 ( 1) 1 ( 1) 0.24 100.00 0.48
==[REG-TOTAL]== 1940 ( 23) 59 ( 23) 1.19 38.98 2.30
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==[ALL-TOTAL]== 3520 ( 376) 552 ( 376) 10.68 68.12 18.47
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 19) 23 ( 19) 10.92 82.61 19.29
Binding 398 ( 50) 77 ( 50) 12.56 64.94 21.05
Gene_expression 722 ( 225) 295 ( 225) 31.16 76.27 44.25
Transcription 137 ( 19) 38 ( 19) 13.87 50.00 21.71
Protein_catabolism 14 ( 4) 7 ( 4) 28.57 57.14 38.10
Phosphorylation 135 ( 48) 53 ( 48) 35.56 90.57 51.06
==[EVT-TOTAL]== 1580 ( 365) 493 ( 365) 23.10 74.04 35.21
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Regulation 338 ( 9) 15 ( 9) 2.66 60.00 5.10
Positive_regulation 1186 ( 15) 43 ( 15) 1.26 34.88 2.44
Negative_regulation 416 ( 1) 1 ( 1) 0.24 100.00 0.48
==[REG-TOTAL]== 1940 ( 25) 59 ( 25) 1.29 42.37 2.50
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==[ALL-TOTAL]== 3520 ( 390) 552 ( 390) 11.08 70.65 19.16
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Task 2
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Task 3
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