Table 2.

Entities automatically extracted by the AFP pipeline

Entity type	Example	Threshold	Special rules
Genes (including protein and sequence names)	lin-3; LIN-3; F36H1.4	2	1. Matched as original keyword or uppercase (proteins)
			2. A single mention in the title is considered a true positive.
Alleles	n1059; sy53; s1263	2	A single mention in the title is considered a true positive.
Strains	CB1417, MT1348	1
Transgenes	syIs107; zhEx68	1
Species	C. elegans, D. rerio, D. melanogaster	10	1. Additional aliases for some species (e.g. human, zebrafish)
			2. A single mention in the title is considered a true positive.