Relation extraction between bacteria and biotopes from biomedical texts with attention mechanisms and domain-specific contextual representations

摘要

Due to the rapid development of computational and biological technology, the biomedical literature is expanding at an exponential rate [ ]. This situation leads to difficulty manually extracting the required information. In BioNLP-ST 2016, the Bacteria Biotope (BB) task [ ] followed the general outline and goals of previous tasks defined in 2011 [ ] and 2013 [ ]. This task aims to investigate the interactions of bacteria and its biotope; habitats or geographical entity, from genetic, phylogenetic, and ecology perspectives. It involves the _ relation, which is a mandatory relation between related arguments, the bacteria and the location where they live. Information pertaining to the habitats where bacteria live is particularly critical in applied microbiology fields such as food safety, health sciences, and waste processing [ – ]. An example relation between bacteria and their location in this task is shown in Fig.  .