Clinical Decision Support Systems (CDSS) utilize computerized Clinical Practice Guidelines (CPG) to deliver evidence-based care recommendations. However, when dealing with comorbidity (i.e., patients with multiple conditions), disease-specific CPG often interact in adverse ways (e.g., drug-drug, drug-disease interactions), and may involve redundant elements as well (e.g., repeated care tasks). To avoid adverse interactions and optimize care, current options involve the static, a priori integration of comorbid CPG by replacing or removing therapeutic tasks. Nevertheless, many aspects are relevant to a clinically safe and efficient integration, and these may change over time–task delays, test outcomes, and health profiles–which are not taken into account by static integrations. Moreover, in case of comorbidity, clinical practice often demands nuanced solutions, based on current health profiles. We propose an execution-time approach to safely and efficiently cope with comorbid conditions, leveraging knowledge from medical Linked Open Datasets to aid during CIG integration.