Learning the Species of Biomedical Named Entities from Annotated Corpora

In biomedical articles, terms with the same surface forms are often used to refer to different entities across a number of model organisms, in which case determining the species becomes crucial to term identification systems that ground terms to specific database identifiers. This paper describes a rule-based system that extracts ‘species indicating words’, such as human or murine, which can be used to decide the species of the nearby entity terms, and a machine-learning species disambiguation system that was developed on manually speciesannotated corpora. Performance of both systems were evaluated on gold-standard datasets, where the machine-learning system yielded better overall results.