clulab / reach

Reach Biomedical Information Extraction
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A sign error #501

Open ozgunbabur opened 7 years ago

ozgunbabur commented 7 years ago

In the below output, the sentence says that PKCalpha does something by phosphorylating fascin (should be positive-regulation), but the sign is falsely inferred as negative-regulation probably because of the complexity of the sentence.

        {
            "predicate": {
                "id": "evem-PMC3935447-UAZ-r1-3935447-163-2",
                "type": "regulation",
                "event_text": "PKCalpha inhibits the formation of nascent adhesions and cell protrusions by phosphorylating fascin",
                "sign": "positive",
                "sub_type": "negative-regulation"
            },
            "participant_a": [
                {
                    "entity_text": "PKCalpha",
                    "entity_type": "protein",
                    "identifier": "uniprot:P17252"
                }
            ],
            "participant_b": [
                {
                    "predicate": {
                        "id": "evem-PMC3935447-UAZ-r1-3935447-163-3",
                        "type": "protein-modification",
                        "event_text": "phosphorylating fascin",
                        "sign": "positive",
                        "sub_type": "phosphorylation"
                    },
                    "participant_b": [
                        {
                            "entity_text": "fascin",
                            "entity_type": "protein",
                            "identifier": "uniprot:Q16658"
                        }
                    ],
                    "sentence": "Fibronectin mediated activation of PKCalpha inhibits the formation of nascent adhesions and cell protrusions by phosphorylating fascin ( at Ser 39 ) to block its association with actin and thereby its functioning in F-actin polymerization ( XREF_BIBR ) ."
                }
            ],
            "sentence": "Fibronectin mediated activation of PKCalpha inhibits the formation of nascent adhesions and cell protrusions by phosphorylating fascin ( at Ser 39 ) to block its association with actin and thereby its functioning in F-actin polymerization ( XREF_BIBR ) ."
        },
MihaiSurdeanu commented 7 years ago

@danebell: this is a negation detection issue, where "inhibits" is incorrectly modifying "phosphorylating". If it's a syntax issue, not much we can do... BUT, it may be from our semantic negation detection code. Please check.