Allergic reactions to medication range from mild to severe or even life-threatening. Proper documentation of patient allergy information is critical for safe prescription, avoiding drug interactions, and reducing healthcare costs. Allergy information is regularly obtained during the medical interview, but is often poorly documented in electronic health records (EHRs). While many EHRs allow for structured adverse drug reaction (ADR) reporting, a free-text entry is still common. The resulting information is neither interoperable nor easily reusable for other applications, such as clinical decision support systems and prescription alerts. Current approaches require pharmacists to review and code ADRs documented by healthcare professionals. Recently, the effectiveness of machine algorithms in natural language processing (NLP) has been widely demonstrated. Our study aims to develop and evaluate different NLP algorithms that can encode unstructured ADRs stored in EHRs into institutional symptom terms. Our dataset consists of 79,712 pharmacist-reviewed drug allergy records. We evaluated three NLP techniques: Naive Bayes-Support Vector Machine (NB-SVM), Universal Language Model Fine-tuning (ULMFiT), and Bidirectional Encoder Representations from Transformers (BERT). We tested different general-domain pre-trained BERT models, including mBERT, XLM-RoBERTa, and WanchanBERTa, as well as our domain-specific AllergyRoBERTa, which was pre-trained from scratch on our corpus. Overall, BERT models had the highest performance. NB-SVM outperformed ULMFiT and BERT for several symptom terms that are not frequently coded. The ensemble model achieved an exact match ratio of 95.33%, a F1 score of 98.88%, and a mean average precision of 97.07% for the 36 most frequently coded symptom terms. The model was then further developed into a symptom term suggestion system and achieved a Krippendorff's alpha agreement coefficient of 0.7081 in prospective testing with pharmacists. Some degree of automation could both accelerate the availability of allergy information and reduce the efforts for human coding.