To enable the vision of precision medicine, evidence-based medicine is the key element. Understanding the natural history of complex diseases like brain aneurysm and particularly investigating the evidences of its rupture risk factors relies on the existence of semantic-enabled data preparation technology to conduct clinical trials, survival analysis and outcome prediction. For personalized medicine in the field of neurological diseases, it is very important that multiple health organizations coordinate and cooperate to conduct evidence based observational studies. Without the means of automating the process of privacy and semantic-enabled data preparation to conduct observational studies at intra-organizational level would require months to manually prepare the data. Therefore, this paper proposes a semantic and privacy enabled, multi-party data preparation architecture and a four-tiered semantic similarity algorithm. Evaluation shows that proposed algorithm achieves a precision of 79%, high recall at 83% and F-measure of 81%.