A dictionary- and rule-based system for identification of bacteria and habitats in text

The number of scientific papers published each year is growing exponentially and given the rate of this growth, automated information extraction is needed to efficiently extract information from this corpus. A critical first step in this process is to accurately recognize the names of entities in text. Previous efforts, such as SPECIES, have identified bacteria strain names, among other taxonomic groups, but have been limited to those names present in NCBI taxonomy. We have implemented a dictionary-based named entity tagger, TagIt, that is followed by a rule based expansion system to identify bacteria strain names and habitats and resolve them to the closest match possible in the NCBI taxonomy and the OntoBiotope ontology respectively. The rule based post processing steps expand acronyms, and extend strain names according to a set of rules, which captures additional aliases and strains that are not present in the dictionary. TagIt has the best performance out of three entries to BioNLP-ST BB3 cat+ner, with an overall SER of 0.628 on the independent test set.