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Table 9 Span detection F1 score results for all algorithms tested against the core + extensions evaluation annotation set of the 30 held-out articles

From: Concept recognition as a machine translation problem

Ontology

CRF

BioBERT

ChEBI_EXT

0.8802

0.9291*

CL_EXT

0.8000

0.9677*

GO_BP_EXT

0.8800*

0.8516

GO_CC_EXT

0.8667

0.9524*

GO_MF_EXT

0.9211

0.9231*

MOP_EXT

> 0.9999*

> 0.9999*

NCBITaxon_EXT

0.9959*

0.9919

PR_EXT

0.5598

0.7717*

SO_EXT

0.8054

0.8244*

UBERON_EXT

0.8418

0.9157*

  1. The best-performing algorithm per ontology is bolded with an asterisk*