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The Specimen Data Refinery:A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections

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Data Intelligence 2022年第2期4卷 320-341页

作者： Alex Hardisty Paul Brack Carole Goble Laurence Livermore Ben Scott Quentin Groom stuart owen Stian Soiland-Reyes School of Computer Science and Informatics Cardiff UniversityCardiff CF243AAUK The Department of Computer Science The University of ManchesterManchester M139PLUK The Natural History Museum London SW75BDUK Meise Botanic Garden 1860 MeiseBelgium Informatics Institute Faculty of ScienceUniversity of Amsterdam1090 GH AmsterdamThe Netherlands

A key limiting factor in organising and using information from physical specimens curated in natural science collections is making that information computable,with institutional digitization tending to focus more on imaging the specimens themselves than on efficiently capturing computable data about *** data are traditionally manually transcribed today with high cost and low throughput,rendering such a task constrained for many collection-holding institutions at current funding *** show how computer vision,optical character recognition,handwriting recognition,named entity recognition and language translation technologies can be implemented into canonical workflow component libraries with findable,accessible,interoperable,and reusable(FAIR)*** libraries are being developed in a cloudbased workflow plaform-the Specimen Data Refinery'(SDR)-founded on Galaxy workflow engine,Common Workflow Language,Research Object Crates(RO-Crate)and WorkflowHub *** SDR can be applied to specimens'labels and other artefacts,offering the prospect of greatly accelerated and more accurate data capture in computable *** kinds of FAIR Digital Objects(FDO)are created by packaging outputs of SDR workflows and workflow components as digital objects with metadata,a persistent identifier,and a specific type *** first kind of FDO are computable Digital Specimen(DS)objects that can be consumed/produced by workflows,and other applications.A single DS is the input data structure submitted to a workflow that is modified by each workflow component in turn to produce a refined DS at the *** Specimen Data Refinery provides a library of such components that can be used individually,or in *** cofunction,each library component describes the fields it requires from the DS and the fields it will in turn populate or *** second kind of FDO,RO-Crates gather and archive the diverse set of digital and real-world resources,configurations,a

关键词： Digital Specimen Workflow FAIR Digital Object RO-Crate

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