BioCreative III interactive task: an overview

BMC Bioinformatics

Table 5 Example of an article containing multiple gene and specie mentions (PMC2680910)

PMCID2680910			Central Vote	Curated Output^a					System Raw Output Team
Gene ID	Gene names	Species		1	2	3	4	5	78	68	65	93	89
10015	ALIX	human	7	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C
57630	POSH	human	7	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C	Y, C
155030	Gag	HIV-1	6	Y, C	Y, C	-	Y, C	Y, C	Y, C	-	-	Y, C	-
36990	POSH	Drosophila		Y	Y	Y	Y	Y	Y	Y	-	Y	Y
43330	ALIX	Drosophila		Y	Y	Y	Y	Y	Y	Y	-	-	Y
128866	CHMP4B	human		Y	Y	Y	Y	-	Y	-	Y	-	Y
39659	TAK-1	Drosophila		Y	Y	Y	Y	Y	-	Y	-	-	Y
3355106	ALG-2	Drosophila		Y	Y	Y	Y	Y	-	-	-	Y	-
7323	UbcH5c	human		Y	Y	Y	Y	-	-	Y	Y	-	-
1489984	p9	EIAV		Y	Y	Y	Y	-	-	-	-	-	-
137492	HCRP1	human		Y	Y	Y	Y	-	Y	-	Y	-	-
7251	TSG101	human		Y	Y	Y	Y	-	Y	-	Y	-	-
155030	p6	HIV-1		Y	-	Y	Y	-	-	-	-	-	-
7334	UBC13	human	1	Y	-	Y, C	Y	-	Y	Y	Y	-	-
	Total genes detected			14	19	13	26	10	90	22	120	9	52
		FP		0	5	0	0	3	81	15	113	4	46
		FN		0	2	1	0	7	5	7	7	8	8
		TP		14	12	13	14	7	9	7	7	5	6
		Precision		1.00	0.71	1.00	1.00	0.70	0.10	0.32	0.06	0.56	0.12
		Recall		1.00	0.86	0.93	1.00	0.50	0.64	0.50	0.50	0.38	0.43

List of Entrez Gene ID, gene name and species found in PMC2680910. The Central Vote column indicates the number of curators that selected the gene as central; “Y”: gene mentioned in the article is detected; “-”:gene mentioned was missed; “C”=indicates central gene as determined by majority vote, and in the systems it means that the gene was ranked high by the system (gene ranked higher than non central genes); “Total genes detected”: totality of gene mentions provided by a given system (what the system considered a gene). FP and FN stand for false positive and negative, respectively. ^aCurated output by manual curation (2 curators, 1-2) and system-assisted curation (5 curators, but 3 are shown, 3-5).

ISSN: 1471-2105