Starting from an experience report on developing ontologies and ontology design patterns for a variety of domains and purposes, this talk will reflect on the complex relationship between Linked Data, cyberinfrastructure, and ontologies. I will discuss the role of modularization and patterns for ontology engineering, technical and social challenges in the adoption of the developed ontologies, and common misunderstandings about interoperability and semantic heterogeneity. Based on this overview, I will outline three new perspectives and argue how they can address some of the outlined challenges.