Much of the existing research about open source elects to study software repositories instead of ecosystems. An open source repository most often refers to the artifacts recorded in a version control system and occasionally includes interactions around the repository itself. An open source ecosystem refers to a collection of repositories, the community, their interactions, incentives, behavioral norms, and culture. The decentralized nature of open source makes holistic analysis of the ecosystem an arduous task, with communities and identities intersecting in organic and evolving ways. Despite these complexities, the increased scrutiny on software security and supply chains makes it of the utmost importance to take an ecosystem-based approach when performing research about open source. This talk provides guidelines and best practices for research using data collected from open source ecosystems, encouraging research teams to work with communities in respectful ways.