The BioLexicon: a large-scale terminological resource for biomedical text mining

BMC Bioinformatics

Table 2 Top level NE categories

NE class	Definition
DNA	Entities chiefly composed of nucleic acids and their structural or positional references. This includes the physical structure of all DNA-based entities and the functional roles associated with regions thereof.
PROTEIN	Entities chiefly composed of amino acids and their positional references. This includes the physical structure and functional roles associated with each type.
EXPERIMENTAL	Both physical and methodological entities, either used, consumed or required for a reaction to take place.
ORGANISMS	Entities representing individuals or collections of living things and their component parts.
PROCESSES	A set of event classes used to label biological processes described in text.

The NE taxonomy used during event annotation is organised into 5 top-level classes, each of which contains a hierarchically structured set of more specific terms. Annotators were instructed to assign the most specific term possible. The general definition of each top-level class is shown in the table.

ISSN: 1471-2105