OntoBiotope-BioNLP-OST

This version OntoBiotope-BioNLP-OST is a subset of the OntoBiotope ontology. created for the Bacteria Biotope task of BioNLP-OST 2019 competition. OntoBiotope is an ontology of microorganism habitats. Its modeling principle and its lexicon reflect the biotope and the phenotype classification used by biologists to describe microorganism isolation sites (e.g. GenBank, GOLD, ATCC). OntoBiotope is developed and maintained by the Meta-omics of Microbial Ecosystems (MEM) network in which 30 microbiologists from INRA (French National Institute for Agricultural Research) from all fields of applied microbiology participate. The relevance of OntoBiotope terms is evaluated through the PubMedBiotope semantic search engine. It identifies and categorizes microbial biotopes in all PubMed abstracts by applying the ToMap method (Text to Ontology Mapping) to the OntoBiotope ontology. It also indexes 3,35 millions relations between taxa and their habitats.