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Table 1 Five keyword dependency patterns and examples

From: The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature

Relation

Type

Explanation

Dependency pattern example

Sample sentence

nsubj(A,B)

B is nominal subject of A

nsubj(control, expression)

The expression of rsfA is under the control of both sigma(F) and sigma(G)

nsubjpass(A, B)

B is passive nominal subject of A

nsubjpass(recognized, promoter)

The ald promoter, like the sigE promoter, is believed to be recognized by sigmaA RNA polymerase, suggesting that sigmaK may inhibit sigmaA activity late in sporulation.

dobj(A, B)

B is direct object of A

dobj(inhibit, activity)

The ald promoter, like the sigE promoter, is believed to be recognized by sigmaA RNA polymerase, suggesting that sigmaK may inhibit sigmaA activity late in sporulation.

amod(A,B)

B is adjectival modifier of A

amod(transcription, GeneX-dependent)

These results demonstrate that sigmaK-dependent transcription of gerE initiates a negative feedback loop in which GerE acts as a repressor to limit production of sigmaK.

nmod(A,B)

B is nominal modifier of A

nmod(essential, expression)

Both SigK and GerE were essential for ykvP expression, and this gene was transcribed from T5 of sporulation.