Table 2.

Examples of the transcription of BioNLP annotations into BioC XML format

Annotation category	BioNLP annotation
	BioC transcription
Entities	T1 Protein 19 49 interferon regulatory factor 4
	<annotation id="T1"><infon key="typeUri">uima:ts:uk.ac . . . . bionlpst.Entity</infon><infon key="type">Entity</infon><infon key="category">Protein</infon><location offset="19” length="30"/><text>interferon regulatory factor 4</text></annotation>
Events with modifications	T11 Gene_expression 55 65 expressionE2 Gene_expression:T11 Theme:T1M1 Speculation E2
	<annotation id="TRIGGER_55_65"><infon key="type">Trigger</infon><location offset="55” length="10"/><text>expression</text></annotation><relation id="E2"><infon key="typeUri">uima:ts:uk.ac . . . .bionlpst.Event</infon><infon key="type">Event</infon><infon key="category">Gene_expression</infon><infon key="negation">false</infon><infon key="speculation">true</infon><node refid="TRIGGER_55_65” role="EventTrigger"/><node refid="T1” role="Theme"/></relation>
Equivalent entities	* Equiv T2 T3
	<relation id="EE53"><infon key="typeUri">uima:ts:uk . . . .EquivalentEntities</infon><infon key="type">Equivalent</infon><node refid="T2” role=""/><node refid="T3” role=""/></relation>
Coreferences (GENIA corpora)	R1 Coreference Subject:T13 Object:T3R2 Coreference Subject:T13 Object:T4R3 Coreference Subject:T13 Object:T5
	<relation id="RT13"><infon key="typeUri">uima:ts:uk.ac . . . .cas.bionlpst.Relation</infon><infon key="type">Coreference</infon><node refid="T13” role="Subject"/><node refid="T3” role="Object"/><node refid="T4” role="Object"/><node refid="T5” role="Object"/></relation>