Phosphorylation_token_3_noun fails in some ambiguous cases

[bgyori]

This rule seems to look for X phosphorylation in text and extract an X is phosphorylated event. However, X phosphorylation is ambiguous because it can either mean phosphorylation of X or phosphorylation by X.

Consider the following (simplified) sentences:

• The PTEN protein contains a CK2 phosphorylation site.
• Mutations of the AKT1 phosphorylation site of RUNX3 decreased RUNX3 sumoylation.
• We studied the MEK phosphorlyation site of ERK.

In the above examples, the phosphorylation site is on PTEN, RUNX2 and ERK, respectively. I'm not sure if it's possible but I wonder if some of these exception cases can be handled.

[MihaiSurdeanu]

I thought our grammar handles these situations because we have this rule with higher priority: "X phosphorylation of Y", i.e., when X is a case, which is prioritized higher than "X phosphorylation", where X is the theme. We'll look into this.

[myedibleenso]

"site" is the smoking gun here.