Background: To parse free text medical notes into structured data such as disease names, drugs, procedures, and other important medical information first, it is necessary to detect medical entities. It is important for an Electronic Medical Record (EMR) to have structured data with semantic interoperability to serve as a seamless communication platform whenever a patient migrates from one physician to another. However, in free text notes, medical entities are often expressed using informal abbreviations. An informal abbreviation is a non-standard or undetermined abbreviation, made in diverse writing styles, which may burden the semantic interoperability between EMR systems. Therefore, a detection of informal abbreviations is required to tackle this issue. Objectives: We attempt to achieve highly reliable detection of informal abbreviations made in diverse writing styles. Methods: In this study, we apply the Long Short-Term Memory (LSTM) model to detect informal abbreviations in free text medical notes. Additionally, we use sliding windows to tackle the limited data issue and sample generator for the imbalance class issue, while introducing additional pre-trained features (bag of words and word2vec vectors) to the model. Results: The LSTM model was able to detect informal abbreviations with precision of 93.6%, recall of 57.6%, and F1-score of 68.9%. Conclusion: Our method was able to recognize informal abbreviations using small data set with high precision. The detection can be used to recognize informal abbreviations in real-time while the physician is typing it and raise appropriate indicators for the informal abbreviation meaning confirmation, thus increase the semantic interoperability.