Data mapping among different data standards in health institutes is often a necessity when data exchanges occur among different institutes. However, no matter rule-based approaches or traditional machine learning methods, none of these methods have achieved satisfactory results yet. In this work, we propose a deep learning method, mixture feature embedding convolutional neural network (MfeCNN), to convert the data mapping to a multiple classification problem. Multi-modal features were extracted from different semantic space with a medical NLP package and powerful feature embeddings were generated by MfeCNN. Classes as many as ten were classified simultaneously by a fully-connected soft-max layer based on multi-view embedding. Experimental results show that our proposed MfeCNN achieved best results than traditional state-of-the-art machine learning models and also much better results than the convolutional neural network of only using bag-of-words as inputs.