MOTIVATION: Relation extraction (RE) is a crucial process to deal with the amount of text published daily, e.g. to find missing associations in a database. RE is a text mining task for which the state-of-the-art approaches use bidirectional encoders, namely, BERT. However, state-of-the-art performance may be limited by the lack of efficient external knowledge injection approaches, with a larger impact in the biomedical area given the widespread usage and high quality of biomedical ontologies. This knowledge can propel these systems forward by aiding them in predicting more explainable biomedical associations. With this in mind, we developed K-RET, a novel, knowledgeable biomedical RE system that, for the first time, injects knowledge by handling different types of associations, multiple sources and where to apply it, and multi-token entities. RESULTS: We tested K-RET on three independent and open-access corpora (DDI, BC5CDR, and PGR) using four biomedical ontologies handling different entities. K-RET improved state-of-the-art results by 2.68% on average, with the DDI Corpus yielding the most significant boost in performance, from 79.30% to 87.19% in F-measure, representing a P-value of 2.91×10-12. AVAILABILITY AND IMPLEMENTATION: https://github.com/lasigeBioTM/K-RET.

Biomedical Relation Extraction (RE) systems identify and classify relations between biomedical entities to enhance our knowledge of biological and medical processes. Most state-of-the-art systems use deep learning approaches, mainly to target relations between entities of the same type, such as proteins or pharmacological substances. However, these systems are mostly restricted to what they directly identify on the text and ignore specialized domain knowledge bases, such as ontologies, that formalize and integrate biomedical information typically structured as direct acyclic graphs. On the other hand, Knowledge Graph (KG)-based recommendation systems already showed the importance of integrating KGs to add additional features to items. Typical systems have users as people and items that can range from movies to books, which people saw or read and classified according to their satisfaction rate. This work proposes to integrate KGs into biomedical RE through a recommendation model to further improve their range of action. We developed a new RE system, named K-BiOnt, by integrating a baseline state-of-the-art deep biomedical RE system with an existing KG-based recommendation state-of-the-art system. Our results show that adding recommendations from KG-based recommendation improves the system's ability to identify true relations that the baseline deep RE model could not extract from the text. The code supporting this system is available at https://github.com/lasigeBioTM/K-BiOnt.

BACKGROUND: Recent 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. RESULTS: We propose a new model to detect and classify relations in text, 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 open biomedical ontologies, specifically Chemical Entities of Biological Interest (ChEBI), Human Phenotype, and Gene Ontology. We assessed the performance of BO-LSTM with drug-drug interactions mentioned 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 the F1-score of both the detection and classification of drug-drug interactions, particularly in a document set with a limited number of annotations. We adapted an existing DDI extraction model with our ontology-based method, obtaining a higher F1 score than the original model. Furthermore, we developed and made available a corpus of 228 abstracts annotated with relations between genes and phenotypes, and demonstrated how BO-LSTM can be applied to other types of relations. CONCLUSIONS: 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.