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Microbiology research has access to a very large amount of public informationon the habitats of microorganisms. Many areas of microbiology research usesthis information, primarily in biodiversity studies. However the habitatinformation is expressed in unstructured natural language form, which hindersits exploitation at large-scale. It is very common for similar habitats to bedescribed by different terms, which makes them hard to compare automatically,e.g. intestine and gut. The use of a common reference to standardize thesehabitat descriptions as claimed by (Ivana et al., 2010) is a necessity. Wepropose the ontology called OntoBiotope that we have been developing since2010. The OntoBiotope ontology is in a formal machine-readable representationthat enables indexing of information as well as conceptualization andreasoning.

Text-mining and ontologies: new approaches to knowledge discovery of microbial diversity