Download modifying phrase combination when main verb is an interaction word.

Bio-Medical Interaction
Extractor (IntEx)
Syed Toufeeq Ahmed
ASU
Scopes

Various syntactic roles (such as Subject , Object
and Modifying phrase) and their linguistically
significant combinations makes up SCOPES

A SCOPE MATCHING is:



Elementary (E) : If the scope contains a Gene /Protein (G)
name or an interaction word (I).
Partial (P) : If the scope has a Gene/Protein (G) name and
an interaction word (I).
Complete (C) : If the scope has at least two Gene /Protein
(G) names and an interaction word (I).
Scopes
“HMBA could inhibit the MEC-1 cell proliferation by down-regulation
of PCNA expression.”
Elementary
(Subject)
Interaction
(Verb)
Elementary
(Object)
Partial
(Modifying Phrase)
Scopes & Matches
“The kinase phosphorylation of Gene1 by Gene2 could inhibit Gene3. ”
Complete
(Subject)
Algorithm of Interaction Extractor:
Is
Main Verb
an
Interaction (I)
?
Interaction : { G1, I, G2 }
Interaction : { G1, I, G2 }
S-O
S
Subject
SM
O
Object
Modifying
Phrase
Partial (I,G2)
Elementary (G1)
complete (G,I,G) 
interact: {G,I,G}
M
P
Elementary (G2)
complete (G,I,G) 
interact: {G,I,G}
complete (G,I,G) 
interact: {G,I,G}
Example (show the interaction flying
in)
“HMBA could inhibit the MEC-1 cell proliferation by down-regulation
of PCNA expression.”
{
Main Verb
(I) “down-regulation”,
“HMBA”,
Elementary
(G)
“PCNA expression”}
Elementary
(G)
{ “HMBA”, “inhibit”, “the MEC-1 cell proliferation” }
Partial
Next Steps


Handling negations in the sentences (such as “not
interact”, “fails to induce”, “does not inhibit”).
Extraction of detailed contextual attributes of
interactions (such as bio-chemical context or location)
by interpreting modifiers:





Location/Position modifiers (in, at, on, into, up, over…)
Agent/Accompaniment modifiers (by, with…)
Purpose modifiers( for…)
Theme/association modifiers ( of..)
Extraction of relationships between interactions from
among multiple sentences in abstracts
(signaling pathways)
Next Steps

Visualization of Signaling Pathways
Evaluation (Recall comparison with BioRAT)
IntEx
Results
BioRAT
Cases
Percent
(%)
Cases
Percent
Match
129
19.94
79
20.31
No Match
518
80.06
310
79.67
Totals
647
100.00
389
100.00
Recall comparison of IntEx and BioRAT from 229 abstract
Evaluation (Precision comparison with BioRAT)
IntEx
BioRAT
Results
Cases
Percent (%)
Cases
Percent
Correct
229
54.39
239
55.07
Incorrect
192
45.60
195
44.93
Totals
421
100.00
434
100.00
Precision comparison of IntEx and BioRAT from 229 abstracts.
References

Link Grammar:
http://www.link.cs.cmu.edu/link

LocusLink:
http://www.ncbi.nlm.nih.gov/LocusLink

UMLS:
http://www.nlm.nih.gov/research/umls/umlsmain.html