Bio-Medical Interaction Extractor (IntEx)

1. Bio-Medical Interaction Extractor (IntEx) Syed Toufeeq Ahmed ASU

2. 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 andan interaction word (I).

3. Scopes “HMBA could inhibit the MEC-1 cell proliferation by down-regulation of PCNA expression.” Elementary (Subject) Elementary (Object) Interaction (Verb) Partial (Modifying Phrase)

4. Scopes & Matches “The kinase phosphorylation of Gene1 by Gene2 could inhibit Gene3. ” Complete (Subject)

5. Algorithm of Interaction Extractor: Is Main Verb an Interaction (I) ? Interaction : { G1, I, G2 } Interaction : { G1, I, G2 } S-O S-M S O MP Subject Object Modifying Phrase Elementary (G1) Partial (I,G2) Elementary (G2) complete (G,I,G)  interact: {G,I,G} complete (G,I,G)  interact: {G,I,G} complete (G,I,G)  interact: {G,I,G}

6. Example (show the interaction flying in) “HMBA could inhibit the MEC-1 cell proliferation by down-regulation of PCNA expression.” Main Verb (I) { “HMBA”, “down-regulation”, “PCNA expression”} Elementary (G) Elementary (G) { “HMBA”, “inhibit”, “the MEC-1 cell proliferation” } Partial

7. 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)

8. Next Steps • Visualization of Signaling Pathways

9. Evaluation (Recall comparison with BioRAT) Recall comparison of IntEx and BioRAT from 229 abstract

10. Evaluation (Precision comparison with BioRAT) Precision comparison of IntEx and BioRAT from 229 abstracts.

11. 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