A Data Ecosystem offers a keystone-player or alliance-driven infrastructure that enables the interaction of different stakeholders and the resolution of interoperability issues among shared data. However, despite years of research in data governance and management, trustability is still affected by the absence of transparent and traceable data-driven pipelines. In this work, we focus on requirements and challenges that data ecosystems face when ensuring data transparency. Requirements are derived from the data and organizational management, as well as from broader legal and ethical considerations. We propose a novel knowledge-driven data ecosystem architecture, providing the pillars for satisfying the analyzed requirements. We illustrate the potential of our proposal in a real-world scenario. Lastly, we discuss and rate the potential of the proposed architecture in the fulfillment of these requirements.