Table 1.

Corpora

		AIMed	BioInfer	HPRD50	IEPA	LLL
	size	1955	1100	145	486	77
Entity	scope	human P/G	P/G/R and related	human P/G	Chemicals	P/G
	coverage	all occurrences	all occurrences	NER system	list of 16 names	list of 116 names
	types	no	111 types (ontology)	no	no	P/G
PPI	types	no	68 types (ontology)	no	no	3 types
	binding	no	yes	no	yes	no
	directed	no	yes	no	yes	yes
	complex	no	yes	no	no	no
	negative	no	yes	no	no	no
	certainty	no	no	yes	no	no

Legend:

Size: Number of sentences in the corpus

Entity scope: Types of the named entities identified in the corpus: (P)rotein, (G)ene, (R)NA

Entity coverage: Coverage of in-scope entity occurrences in each sentence

Entity types: Explicit identification of the type of the annotated named entity occurrences

PPI types: Explicit indication of the type of the annotated interactions

PPI binding: Identification of the specific text spans that entail the annotated interactions

PPI directed: Specification of the directionality of the interaction (typically identification of agent vs. patient roles)

PPI complex: Annotation includes nested or n-ary (for n > 2) interactions

PPI negative: Annotation of negative interactions

PPI certainty: Annotation of the levels of certainty, or speculativeness, of interactions