LINNAEUS: A species name identification system for biomedical literature

BMC Bioinformatics

Table 1 Species name tag sets for different evaluation corpora and LINNAEUS output

Tag set	Document set	Documents	Species	Tags
NCBI taxonomy	MEDLINE	5,237	6,871	8,701
	PMC OA abs	10	21	21
	PMC OA	12	26	26
MeSH	MEDLINE	6,817,973	824	7,388,958
	PMC OA abs	44,552	518	51,592
	PMC OA	88,826	527	57,874
Entrez gene	MEDLINE	440,084	3,125	486,791
	PMC OA abs	8,371	406	9,307
	PMC OA	9,327	428	10,294
EMBL	MEDLINE	174,074	149,598	396,853
	PMC OA abs	5,157	7,582	12,775
	PMC OA	7,374	7,867	15,136
PMC linkouts	MEDLINE	35,534	29,351	248,222
	PMC OA abs	41,054	41,070	286,998
	PMC OA	42,910	32,187	289,411
Whatizit-Organisms	MEDLINE	71,856	23,598	3,328,853
	PMC OA abs	82,410 (64,228)	25,375	3,791,412
	PMC OA	94,289	26,557	4,075,644
Manual	MEDLINE	75	176	3,205
	PMC OA abs	89 (76)	215	3,878
	PMC OA	100	233	4,259
LINNAEUS output	MEDLINE	9,919,312	57,802	30,786,517
	PMC OA abs	88,962 (65,739)	5,114	303,146
	PMC OA	105,106	18,943	4,189,681

Numbers in parentheses show the portion of abstracts that can be extracted from the document XML files, enabling mention-level accuracy comparisons (see Methods for details).

ISSN: 1471-2105