Abstract
An experimental protocol describes a sequence of tasks executed to perform experimental research in biological and biomedical areas, e.g. genetics, immunology, neuroscience and virology. Such experimental protocols indicate, for each step, exactly how it should be executed, often including equipment, reagents, descriptions of critical steps, troubleshooting instructions, other kinds of tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. These protocols therefore have a clear systematic structure, but when published they are treated like any other scientific publication i.e. as a narrative text in HTML or PDF format. The formal structure is therefore not easily accessible and cannot be reused. This paper addresses this problem by extracting, representing and publishing steps from experimental protocols to make them Findable, Accessible, Interoperable, and Reusable (FAIR). Our work builds upon human annotations in combination with Named Entity Recognition delivering nanopublications. Our software toolkit, Nanotate, is based on a flexible web based annotation environment, namely Hypothes.is, the BioPortal NER web services and the nanopublications infrastructure. Our evaluation shows that our approach is viable and our tool user-friendly.
Original language | English |
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Title of host publication | Workshop proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences |
Publisher | CEUR Workshop Proceedings |
Pages | 64-73 |
Volume | 3127 |
Publication status | Published - 2022 |
Event | 13th International SWAT4HCLS Conference: Semantic Web Applications and Tools for Health Care and Life Sciences - Leiden (Virtual event), Netherlands Duration: 10 Jan 2022 → 13 Jan 2022 http://www.swat4ls.org/workshops/leiden2022/call-for-papers/ |
Conference
Conference | 13th International SWAT4HCLS Conference |
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Abbreviated title | SWAT4HCLS |
Country/Territory | Netherlands |
City | Leiden (Virtual event) |
Period | 10/01/22 → 13/01/22 |
Internet address |