title: Named entity recognition for bacterial Type IV secretion systems.
abstract: Research on specialized biological systems is often hampered by a lack of consistent terminology, especially across species. In bacterial Type IV secretion systems genes within one set of orthologs may have over a dozen different names. Classifying research publications based on biological processes, cellular components, molecular functions, and microorganism species should improve the precision and recall of literature searches allowing researchers to keep up with the exponentially growing literature, through resources such as the Pathosystems Resource Integration Center (PATRIC, patricbrc.org). We developed named entity recognition (NER) tools for four entities related to Type IV secretion systems: 1) bacteria names, 2) biological processes, 3) molecular functions, and 4) cellular components. These four entities are important to pathogenesis and virulence research but have received less attention than other entities, e.g., genes and proteins. Based on an annotated corpus, large domain terminological resources, and machine learning techniques, we developed recognizers for these entities. High accuracy rates (>80%) are achieved for bacteria, biological processes, and molecular function. Contrastive experiments highlighted the effectiveness of alternate recognition strategies; results of term extraction on contrasting document sets demonstrated the utility of these classes for identifying T4SS-related documents.
authors.affiliation: School of Computer Science, University of Manchester, Manchester, United Kingdom.
authors.forename: Sophia
authors.initials: S
authors.lastname: Ananiadou
authors.forename: Dan
authors.initials: D
authors.lastname: Sullivan
authors.forename: William
authors.initials: W
authors.lastname: Black
authors.forename: Gina-Anne
authors.initials: GA
authors.lastname: Levow
authors.forename: Joseph J
authors.initials: JJ
authors.lastname: Gillespie
authors.forename: Chunhong
authors.initials: C
authors.lastname: Mao
authors.forename: Sampo
authors.initials: S
authors.lastname: Pyysalo
authors.forename: Balakrishna
authors.initials: B
authors.lastname: Kolluru
authors.forename: Junichi
authors.initials: J
authors.lastname: Tsujii
authors.forename: Bruno
authors.initials: B
authors.lastname: Sobral
mesh_terms: D058947:Bacterial Secretion Systems; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated; D009626:Terminology as Topic; D018875:Vocabulary, Controlled
chemical_list: D058947:Bacterial Secretion Systems