Nanotate: Semantically Annotating Experimental Protocols with Nanopublications

Olga Giraldo, Miguel Ruano, Robin A. Richardson, Remzi Celebi, Michel Dumontier, Tobias Kuhn

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademicpeer-review

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 languageEnglish
Title of host publicationWorkshop proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences
PublisherCEUR Workshop Proceedings
Pages64-73
Volume3127
Publication statusPublished - 2022
Event13th International SWAT4HCLS Conference: Semantic Web Applications and Tools for Health Care and Life Sciences - Leiden (Virtual event), Netherlands
Duration: 10 Jan 202213 Jan 2022
http://www.swat4ls.org/workshops/leiden2022/call-for-papers/

Conference

Conference13th International SWAT4HCLS Conference
Abbreviated titleSWAT4HCLS
Country/TerritoryNetherlands
CityLeiden (Virtual event)
Period10/01/2213/01/22
Internet address

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