title: Machine Reading for Extraction of Bacteria and Habitat Taxonomies.
abstract: There is a vast amount of scientific literature available from various resources such as the internet. Automating the extraction of knowledge from these resources is very helpful for biologists to easily access this information. This paper presents a system to extract the bacteria and their habitats, as well as the relations between them. We investigate to what extent current techniques are suited for this task and test a variety of models in this regard. We detect entities in a biological text and map the habitats into a given taxonomy. Our model uses a linear chain Conditional Random Field (CRF). For the prediction of relations between the entities, a model based on logistic regression is built. Designing a system upon these techniques, we explore several improvements for both the generation and selection of good candidates. One contribution to this lies in the extended exibility of our ontology mapper that uses an advanced boundary detection and assigns the taxonomy elements to the detected habitats. Furthermore, we discover value in the combination of several distinct candidate generation rules. Using these techniques, we show results that are significantly improving upon the state of art for the BioNLP Bacteria Biotopes task.
authors.affiliation: Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Avenue, 61801-2302, Urbana, IL, U.S.A., Department of Computer Science, KU Leuven, Celestijnenlaan 200A, 3001, Heverlee, Belgium.
authors.forename: Parisa
authors.initials: P
authors.lastname: Kordjamshidi
authors.affiliation: Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Avenue, 61801-2302, Urbana, IL, U.S.A., Department of Computer Science, KU Leuven, Celestijnenlaan 200A, 3001, Heverlee, Belgium.
authors.forename: Wouter
authors.initials: W
authors.lastname: Massa
authors.affiliation: Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Avenue, 61801-2302, Urbana, IL, U.S.A., Department of Computer Science, KU Leuven, Celestijnenlaan 200A, 3001, Heverlee, Belgium.
authors.forename: Thomas
authors.initials: T
authors.lastname: Provoost
authors.affiliation: Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Avenue, 61801-2302, Urbana, IL, U.S.A., Department of Computer Science, KU Leuven, Celestijnenlaan 200A, 3001, Heverlee, Belgium.
authors.forename: Marie-Francine
authors.initials: MF
authors.lastname: Moens