ArticleBMC bioinformatics2015
Detection and categorization of bacteria habitats using shallow linguistic analysis.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Linking entities through an ontology using word embeddings and syntactic re-ranking.BMC bioinformatics · 2019Article
- COPIOUS: A gold standard corpus of named entities towards extracting species occurrence from biodiversity literature.Biodiversity data journal · 2019Article
- Classification and analysis of a large collection of in vivo bioassay descriptions.PLoS computational biology · 2017Article
- Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations.Briefings in bioinformatics · 2017Article
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2 authors.
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Abstract
backgroundInformation regarding bacteria biotopes is important for several research areas including health sciences, microbiology, and food processing and preservation. One of the challenges for scientists in these domains is the huge amount of information buried in the text of electronic resources. Developing methods to automatically extract bacteria habitat relations from the text of these electronic resources is crucial for facilitating research in these areas.
methodsWe introduce a linguistically motivated rule-based approach for recognizing and normalizing names of bacteria habitats in biomedical text by using an ontology. Our approach is based on the shallow syntactic analysis of the text that include sentence segmentation, part-of-speech (POS) tagging, partial parsing, and lemmatization. In addition, we propose two methods for identifying bacteria habitat localization relations. The underlying assumption for the first method is that discourse changes with a new paragraph. Therefore, it operates on a paragraph-basis. The second method performs a more fine-grained analysis of the text and operates on a sentence-basis. We also develop a novel anaphora resolution method for bacteria coreferences and incorporate it with the sentence-based relation extraction approach.
resultsWe participated in the Bacteria Biotope (BB) Task of the BioNLP Shared Task 2013. Our system (Boun) achieved the second best performance with 68% Slot Error Rate (SER) in Sub-task 1 (Entity Detection and Categorization), and ranked third with an F-score of 27% in Sub-task 2 (Localization Event Extraction). This paper reports the system that is implemented for the shared task, including the novel methods developed and the improvements obtained after the official evaluation. The extensions include the expansion of the OntoBiotope ontology using the training set for Sub-task 1, and the novel sentence-based relation extraction method incorporated with anaphora resolution for Sub-task 2. These extensions resulted in promising results for Sub-task 1 with a SER of 68%, and state-of-the-art performance for Sub-task 2 with an F-score of 53%.
conclusionsOur results show that a linguistically-oriented approach based on the shallow syntactic analysis of the text is as effective as machine learning approaches for the detection and ontology-based normalization of habitat entities. Furthermore, the newly developed sentence-based relation extraction system with the anaphora resolution module significantly outperforms the paragraph-based one, as well as the other systems that participated in the BB Shared Task 2013.
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