Clinical treatments are mostly the result of consecutive success of medical procedures. The patterns in those procedures lead to creation of clinical guidelines which are currently essential to have better health treatments. The use of electronic health record systems (EHR) helps the patient management, but it fails in the treatment guidance due to the lack of clinical decision support systems. Although these systems have decision-making features incorporated, they are not designed for treatment management and guidance. In some top edge systems, this functionality was improved and integrated, but either they are tight to the typically complex EHR. Or, many times the independent solutions lack generality to support users and disease-specific protocols. In this paper, we purpose a decision support web tool which works independently from EHR systems. This solution allows clinicians to build and manage rule-based clinical protocols, by facilitating health care treatments, reducing time, and increasing medication accuracy. Moreover, it also enables protocol sharing among distinct institutions and physicians, creating a larger database of clinical guidelines and a network of speciliased physicians in types of diseases. The proposed system was evaluated with the implementation of distinct clinical protocols, from different medical fields. In this validation, we describe all the steps in the transformation of a clinical guideline, from the traditional format, into a ready-to-use protocol with guidance and recommendation features. The purposed system was developed with the collaboration of health professionals from different Portuguese healthcare institutions, which helped in the identification of system requirements and gaps of the current systems.