Paper: Bacteria Biotope Detection, Ontology-based Normalization, and Relation Extraction using Syntactic Rules

ACL ID W13-2025
Title Bacteria Biotope Detection, Ontology-based Normalization, and Relation Extraction using Syntactic Rules
Venue Proceedings of the BioNLP Shared Task 2013 Workshop
Session
Year 2013
Authors

The absence of a comprehensive database of locations where bacteria live is an im- portant obstacle for biologists to under- stand and study the interactions between bacteria and their habitats. This paper re- ports the results to a challenge, set forth by the Bacteria Biotopes Task of the BioNLP Shared Task 2013. Two systems are ex- plained: Sub-task 1 system for identifying habitat mentions in unstructured biomedi- cal text and normalizing them through the OntoBiotope ontology and Sub-task 2 sys- tem for extracting localization and part- of relations between bacteria and habitats. Both approaches rely on syntactic rules designed by considering the shallow lin- guistic analysis of the text. Sub-task 2 system also makes use of discourse-based rules. The two systems achieve promising result...