This model annotates each word or term in a piece of text with a tag representing the entity type, taken from a list of 145 entity tags from the GENIA Term corpus version 3.02.
These tags cover 36 types of biological named entities:
- protein(family_or_group,complex, molecule, subunit, substructure, domain_or_region, other)
- peptide
- amino_acid_monomer
- DNA/RNA(family_or_group, molecule, substructure, domain_or_region, other),- polynucleotide
- nucleotide
- multi_cell
- mono_cell
- virus
- body_part
- tissue
- cell_type
- cell_component
- cell_line
- other_artificial_source
- lipid
- carbohydrate
- other_organic_compound
- inorganic
- atom
- a tag for 'no entity'
You can refer to the the GENIA corpus—a semantically annotated corpus for bio-textmining for full entity definitions.
The entity types furthermore may be tagged with either a "B-", "I-", "L-", or "U-" tag. A "U-" tag manifests only term of a single-term entity. A "B-" tag indicates the first term of a new multi-term entity, while subsequent middle terms in an entity will have an "I-" tag and the last term will have the "L-" tag. For example, "monocytes" would be tagged as "U-Cell_Type" while "human-immunodeficiency virus type 2" would be tagged as ["B-Virus", "I-Virus", "I-Virus", "I-Virus", "L-Virus"].