Oyster: A tool for fine-grained ontological annotations in free-text

Abstract

Oyster is a web-based annotation tool that allows users to annotate free-text with respect to concepts defined in formal knowledge resources such as large domain ontologies. The tool has been explicitly designed to provide (manual and automatic) search functionalities to identify the best concept entities to be used for annotation. In addition, Oyster supports features such as annotations that span across nonadjacent tokens, multiple annotations per token, the identification of entity relationships and a user-friendly visualisation of the annotation including the use of filtering based on annotation types. Oyster is highly configurable and can be expanded to support a variety of knowledge resources. The tool can support a wide range of tasks involving human annotation, including named-entity extraction, relationship extraction, annotation correction and refinement.