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Background Drug development is an expensive and time-consuming process. Literature-based discovery has played a critical role in drug development and may be a supplementary method to help scientists speed up the discovery of drugs. Methods Here, we propose a relation path features embedding based convolutional neural network model with attention mechanism for drug discovery from literature, which we denote as PACNN. First, we use predications from biomedical abstracts to construct a biomedical knowledge graph, and then apply a path ranking algorithm to extract drug-disease relation path features on the biomedical knowledge graph. After that, we use these drug-disease relation features to train a convolutional neural network model which combined with the attention mechanism. Finally, we employ the trained models to mine drugs for treating diseases. Results The experiment shows that the proposed model achieved promising results, comparing to several random walk algorithms. Conclusions In this paper, we propose a relation path features embedding based convolutional neural network with attention mechanism for discovering potential drugs from literature. Our method could be an auxiliary method for drug discovery, which can speed up the discovery of new drugs for the incurable diseases. Electronic supplementary material The online version of this article (10.1186/s12911-019-0764-5) contains supplementary material, which is available to authorized users.

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