Ontology Based Categorization of Habitat Entities using Information Retrieval Techniques

Gathering information about habitats of bacteria and representing them in a normalized way is the key point of microbiology studies. Having this information spread through textual resources such as

scientific articles and web pages leads to a need for automatically detecting 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 application represents a system for habitat entity normalization through OntoBiotope ontology. In

order to find suitable normalizations for habitats, the system uses cosine similarity with tf-idf scores between ontology concepts and habitats expanded with the document where the habitat placed.