Bio-Medical Interaction Extractor

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

Elementary(Subject) Elementary

(Object)

Partial(Modifying Phrase)

“HMBA could inhibit the MEC-1 cell proliferation by down-regulation of PCNA expression.”

Interaction(Verb)

Scopes & Matches

“The kinase phosphorylation of Gene1 by Gene2 could inhibit Gene3. ”

Complete(Subject)

Algorithm of Interaction Extractor:

S O MP

S-O S-M

Subject Modifying Phrase

Object

complete (G,I,G) interact: {G,I,G}

complete (G,I,G) interact: {G,I,G}

complete (G,I,G) interact: {G,I,G}

Elementary (G1) Elementary (G2)

Is Main Verb

an Interaction (I)

?

Interaction : { G1, I, G2 }

Partial (I,G2)

Interaction : { G1, I, G2 }

Example

Elementary(G)

Elementary(G)

Partial

“HMBA could inhibit the MEC-1 cell proliferation by down-regulation of PCNA expression.”

Main Verb(I)

{ “HMBA”, “inhibit”, “the MEC-1 cell proliferation” }

{ “HMBA”, “down-regulation”, “PCNA expression”}

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

Preliminary Results

Dataset Precision % Recall %

Curated text 95.4 % 95.4 %

Abstracts 91.66 % 89.18 %

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