Applications of Natural Language Processing in Biodiversity Science

Table 3

Existing IE systems for biology [17–26].

System	Approach	Structure of Text	Knowledge in	Application domain	Reference
AkanePPI	shallow parsing	sentence-split, tokenized, and annotated		protein interactions	[17]
EMPathIE	pattern matching	text	EMP database	enzymes	[18]
PASTA	pattern matching	text	biological lexicons	protein structure	[19]
BioIE	pattern matching	xml	dictionary of terms	biomedicine	[20]
BioRAT	pattern matching, sub-language driven	could be xml, html, text or asn.1, can do full-length pdf papers (converts to text)	dictionary for protein and gene names, dictionary for interactions, and synonyms; text pattern template	biomedicine	[21]
Chilibot	shallow parsing	not sure what was used in paper, but could be xml, html, text or asn.1	nomenclature dictionary	biomedicine	[22]
Dragon Toolkit	mixed syntactic semantic	text	domain ontologies	genomics	[23]
EBIMed	pattern matching	xml	dictionary of terms	biomedicine	[24]
iProLINK	shallow parsing	text	protein name dictionary, ontology, and annotated corpora	proteins	[25]
LitMiner	mixed syntactic semantic	web documents		Drosophila research	[26]