Table 7.

Number of entities pre-annotated after extending PubTator annotation with the PHARE ontology.

PHARE entity	Discontiguous	All
Chemical	430	87,764
Disease	0	29,589
Gene_or_protein	4,690	10,1326
Genomic_variation	8,698	13,601
Phenotype	10,935	16,770

Because discontiguous entities are excluded from our baseline experiments (see Section Technical Validation), their number is specified. No disease entity is discontiguously annotated first because PubTator is not generating discontiguous annotation, and second because the extension of annotations with PHARE (which may be discontiguous) is not producing disease annotations, but phenotype annotations.