The BioInfer annotation defines entity and relationship types through two ontologies defined for use in the corpus annotation. These ontologies are included as part of the corpus XML file. A brief description and links to illustrations of the ontologies are also given here.
The relationship ontology
The relationship type ontology defines the bioentity relationships annotated in the BioInfer corpus, organizes them in a hierarchy of relationship types, and defines their arguments. The type of each relationship annotated in the corpus is assigned one of the relationship ontology leaf nodes. The non-leaf nodes in the hierarchical ontology only specify its structure and are not used in the annotation.
An illustration of the ontology is given on the relationship type ontology page.
The entity type ontology
The entity type ontology defines the types of entities annotated in the corpus, organizing them hierarchically. The entity type ontology incorporates in its physical entity subtree the GENIA ontology of physical entities, extending it in part according to BioInfer annotation needs. The entity type ontology also includes two other main subtrees: the the process subtree, which mirrors the BioInfer relationship type ontology, and the property subtree, which defines the main properties associated with entity state.
An illustration of the ontology is given on the entity type ontology page.