AbstractRecent studies have proposed deep learning techniques, namely recurrent neural networks, to improve biomedical text mining tasks. However, these techniques rarely take advantage of existing domain-specific resources, such as ontologies. In Life and Health Sciences there is a vast and valuable set of such resources publicly available, which are continuously being updated. Biomedical ontologies are nowadays a mainstream approach to formalize existing knowledge about entities, such as genes, chemicals, phenotypes, and disorders. These resources contain supplementary information that may not be yet encoded in training data, particularly in domains with limited labeled data.We propose a new model, BO-LSTM, that takes advantage of domain-specific ontologies, by representing each entity as the sequence of its ancestors in the ontology. We implemented BO-LSTM as a recurrent neural network with long short-term memory units and using an open biomedical ontology, which in our case-study was Chemical Entities of Biological Interest (ChEBI). We assessed the performance of BO-LSTM on detecting and classifying drug-drug interactions in a publicly available corpus from an international challenge, composed of 792 drug descriptions and 233 scientific abstracts. By using the domain-specific ontology in addition to word embeddings and WordNet, BO-LSTM improved both the F1-score of the detection and classification of drug-drug interactions, particularly in a document set with a limited number of annotations. Our findings demonstrate that besides the high performance of current deep learning techniques, domain-specific ontologies can still be useful to mitigate the lack of labeled data.Author summaryA high quantity of biomedical information is only available in documents such as scientific articles and patents. Due to the rate at which new documents are produced, we need automatic methods to extract useful information from them. Text mining is a subfield of information retrieval which aims at extracting relevant information from text. Scientific literature is a challenge to text mining because of the complexity and specificity of the topics approached. In recent years, deep learning has obtained promising results in various text mining tasks by exploring large datasets. On the other hand, ontologies provide a detailed and sound representation of a domain and have been developed to diverse biomedical domains. We propose a model that combines deep learning algorithms with biomedical ontologies to identify relations between concepts in text. We demonstrate the potential of this model to extract drug-drug interactions from abstracts and drug descriptions. This model can be applied to other biomedical domains using an annotated corpus of documents and an ontology related to that domain to train a new classifier.
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