clulab / reach

Reach Biomedical Information Extraction
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Missing complexes and Phosphorylation with obvious patterns #370

Open myedibleenso opened 8 years ago

myedibleenso commented 8 years ago

Until recently, we detected two complexes (Bindings) and a Positive_regulation (Phosphorylation with a controller) in this sentence from PMC3337673:

In mammals, in the presence of RASSF1A and a DNA damage signal, LATS1 phosphorylation of YAP maintains a pool of YAP in the nucleus which switches binding partner from the antiapoptotic, YAP-TEAD complex to a proapoptotic YAP-p73 complex [XREF_BIB].

While we find all of the needed entities, we fail to find any event. We should something for "YAP-TEAD complex", "YAP-p73 complex", and " LATS1 phosphorylation of YAP". Surface patterns should suffice for the two Bindings:

(34,YAP,NN), (35,and,CC), (36,TEAD,NN), (37,complex,NN), (38,to,TO), (39,a,DT), (40,proapoptotic,JJ), (41,YAP,NN), (42,and,CC), (43,p73,NN), (44,complex,NN),

    34:
    35:
    36:
    37: (31,det) (32,nn) (34,nn) (36,nn) (41,prep_to) (44,conj_and)
    38:
    39:
    40:
    41: (39,det) (40,amod)
    42:
    43:
    44: (43,nn) (46,dep)

Given the parse, it is unclear to me why the phosphorylation (Positive_regulation) isn't being found (Phosphorylation_syntax_1_noun used to find this regulation):

    14:
    15: (14,nn) (17,prep_of)
    16:
    17:
(14,LATS1,NN), (15,phosphorylation,NN), (16,of,IN), (17,YAP,NNP)
myedibleenso commented 8 years ago

The phosphorylation bug may have been introduced in https://github.com/clulab/reach/commit/beb7024045f8a140d5429833cb2934829e0a004a, @danebell.