Scientific research is increasingly characterised by the volume of documents and data that it produces, from experimental plans and raw data to reports and papers. Researchers frequently struggle to manage and curate these materials, both individually and collectively. Previous studies of Electronic Lab Notebooks (ELNs) in academia and industry have identified semantic web technologies as a means for organising scientific documents to improve current workflows and knowledge management practices. In this paper, we present a qualitative, user-centred study of researcher requirements and practices, based on a series of discipline-specific focus groups. We developed a prototype semantic ELN to serve as a discussion aid for these focus groups, and to help us explore the technical readiness of a range of semantic web technologies. While these technologies showed potential, existing tools for semantic annotation were not well-received by our focus groups, and need to be refined before they can be used to enhance current researcher practices. In addition, the seemingly simple notion of “tagging and searching” documents appears anything but; the researchers in our focus groups had extremely personal requirements for how they organise their work, so the successful incorporation of semantic web technologies into their practices must permit a significant degree of customisation and personalisation.Electronic supplementary materialThe online version of this article (10.1186/s13321-019-0345-8) contains supplementary material, which is available to authorized users.