Ontology-based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques

Abstract

A database which provides information about bacteria and their habitats in a comprehensive and normalized way is crucial for applied microbiology studies. Having this information spread through textual resources such as scientific articles and web pages leads to a need for automatically detecting bacteria and habitat entities in text, semantically tagging them using ontologies, and finally extracting the events among them. These are the challenges set forth by the Bacteria Biotopes Task of the BioNLP Shared Task 2016. This paper describes a system for habitat and bacteria entity normalization through the OntoBiotope ontology and the NCBI taxonomy, respectively. The system, which obtained promising results on the shared task data set, utilizes basic information retrieval techniques.