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How can authors using many individual pieces of qualitative data throughout a publication make their research transparent? In this paper we introduce Annotation for Transparent Inquiry (ATI), an approach to enhance transparency in qualitative research. ATI allows authors to connect specific passages in their publication with an annotation. These annotations provide additional information relevant to the passage and, when possible, include a link to one or more data sources underlying a claim; data sources are housed in a repository. After describing ATI’s conceptual and technological implementation, we report on its evaluation through a series of workshops conducted by the Qualitative Data Repository (QDR) and present initial results of the evaluation. The article ends with an outlook on next steps for the project.