Assessment of disease named entity recognition on a corpus of annotated sentences

Jimeno, Antonio; Jimenez-Ruiz, Ernesto; Lee, Vivian; Gaudan, Sylvain; Berlanga, Rafael; Rebholz-Schuhmann, Dietrich

doi:10.1186/1471-2105-9-S3-S3

BMC Bioinformatics

Table 4 Recognition of disease in sentences; without the most frequent diseases.

From: Assessment of disease named entity recognition on a corpus of annotated sentences

	Benchmark	Diseases	Annotated	Diseases	FP	TP	Recall	Precision	F-measure
D look-up	586	269	542	217	143	399	68.09	73.62	70.74
Statistical	586	269	760	299	313	447	76.28	58.82	66.42
MetaMap	586	269	413	182	95	318	54.27	77.00	63.66
Vote 1	586	269	908	347	398	510	87.03	56.17	68.27
Vote 2	586	269	532	218	123	409	69.80	76.88	73.17
Vote 3	586	269	278	130	30	248	42.32	89.21	57.41

This table shows the total number of diseases in the benchmark (Benchmark), the number of distinct diseases (Diseases), the number of diseases annotated by the method and the number of unique diseases identified. Then we present the result on standard measures like precision and recall.

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ISSN: 1471-2105

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