2. BioNLP'09 Task 1
Events in abstracts
Given: gene and gene products (proteins)
Wanted: events
type
−
trigger
−
participant(s)
−
cause (if applicable)
−
3. Example
quot;I kappa B/MAD3 masks the nuclear localization
signal of NFkappa B p65 and requires the
transactivation domain to inhibit NFkappa B
p65 DNA binding. quot;
Event: negative regulation
Trigger: masks
Theme1: the first p65
Cause: MAD3
8. CRF features for each token
isprotein
isPPIword
generic POS tag
logfrequency of token being a trigger for each
event type (10 features)
number of proteins in sentence (sentencelevel)
9. Trigger Detection Post Processing
Positive discrimination
Manually looking at false negatives
−
Adding recurring triggers
−
Negative discrimination
Manually looking at false positives
−
Filtering out common mistaken tokens
−
10. Trigger Detection Results
Event Class #Gold R P Fscore
Localisation 40 77.5 47.69 59.05
Binding 180 33.33 54.55 41.38
Gene expression 282 76.6 58.54 66.36
Transcription 68 58.82 18.6 28.27
88.89 86.49
Protein catabolism 19 84.21
97.5 81.25 88.64
Phosphorylation 40
Nonreg total 629 63.91 48.73 55.3
Regulation 138 13.04 62.07 21.56
Positive regulation462 13.85 54.24 22.07
Neg. regulation 153 29.41 45.92 35.86
All total 1382 38.28 49.44 43.15
11. 2) Finding Participants
Type and number of participants
1 theme (protein)
− 1 theme and 1 cause
−
(proteins/other events)
Gene expression
Transcription Regulation
Protein Catabolism Positive regulation
Localisation Negative regulation
Phosphorylation
1 or more themes (protein)
−
Binding
14. Theme in Subtree
Single Theme events
Theme in subtree 0.7054
−
Theme not in subtree 0.2946
−
Binding event
Any theme in subtree = 0.5435
−
Any theme not in subtree = 0.4565
−
Regulation events
Either theme or cause in subtree = 0.5919
−
Either theme or cause not in subtree = 0.4081
−
17. Rules Concerning Parse Tree Analysis
For quot;bindingquot;, report as themes:
up to the second closest protein in the subtree
−
and the first closest protein in the rest of the tree
−
quot;In contrast, gp41 failed to stimulate NFkappaB
binding activity in as much as no NFkappaB bound to
the main NFkappaBbinding site 2 of the IL10
promoter after addition of gp41.quot;
Successfully missing out the final
gp41.
18. Example of a Missed (FN) Theme
For gene expression
All the proteins in the subtree are reported as
−
themes
quot;The 15lipoxygenase (lox) gene is expressed in a
tissuespecific manner, predominantly in
erythroid cells but also in airway epithelial
cells and eosinophils.quot;
is
/
gene expressed
|
15lipoxygenase
19. Evaluation on Development Data
Event Class #Gold R P Fscore
Localisation 53 67.92 46.75 55.38
Binding 312 21.47 63.81 32.13
Gene expression 356 64.61 76.33 69.98
89.8
Transcription 82 53.66 67.18
77.55
Protein catabolism 21 90.48 67.86
91.49
Phosphorylation 47 53.09 67.19
Nonreg total 871 50.4 68.44 58.05
Regulation 172 5.23 33.33 9.05
Positive regulation 632 3.48 21.36 5.99
Neg. regulation 201 9.45 15.08 11.62
Regulatory total 1005 4.98 19.53 7.93
All total 1876 26.07 54.46 35.26
20. Evaluation on Test Data
Event Class #Gold R P Fscore
Localisation 174 44.83 53.06 48.6
Binding 347 12.68 40.37 19.3
722 52.63 69.34 59.84
Gene expression
Transcription 137 15.33 67.74 25
Protein catabolism 14 42.86 50 46.15
135 78.52 53.81 63.86
Phosphorylation
Nonreg total 1529 41.53 60.82 49.36
Regulation 291 3.09 19.15 5.33
Positive regulation 983 1.12 8.87 1.99
Neg. regulation 379 12.4 20.52 15.46
Regulatory total 1653 4.05 16.75 6.53
All total 3182 22.06 48.61 30.35
23. Other Tasks
Event detection and characterization
Event argument recognition
Negations and speculations
24. Example
quot;I kappa B/MAD3 masks the nuclear localization
signal of NFkappa B p65 and requires the
transactivation domain to inhibit NFkappa B
p65 DNA binding. quot;
Event: negative regulation
Trigger: masks
Theme1: the first p65
Cause: MAD3
Site: nuclear localization signal
25. Example
quot;In contrast, NFkappa B p50 alone fails to
stimulate kappa Bdirected transcription, and
based on prior in vitro studies, is not
directly regulated by I kappa B. quot;
Event: regulation
Theme1: this p50
Trigger: regulated
Negation: true for this event
Speculation: none