Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Donat Agosti (agosti@plazi.org)
Received: 19 Aug 2022 | Published: 23 Aug 2022
© 2022 Reto Gmür, Donat Agosti, Guido Sautter
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Gmür R, Agosti D, Sautter G (2022) Synospecies, a Linked Data Application to Explore Taxonomic Names. Biodiversity Information Science and Standards 6: e93707. https://doi.org/10.3897/biss.6.93707
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Synospecies is a linked data application to explore changes in taxonomic names (
While these transformations have been taking place for a long time now, Plazi is now experimenting with making this process more transparent: with the Plazi Actionable Accessible Archive (PAAA) architecture both addition and modification of the digitalized treatments trigger an extensible set of workflows that are immediately executed on the GitHub platform. Not only is the exact definition and code of every workflow publicly accessible, but the results, errors and execution time of every single workflow is accessible as well. This offers an unprecedented degree of transparency and flexibility in the data processing that we have prototypically implemented for the creation of the RDF data used by Synospecies. As with the W3C GRDDL recommendation (https://www.w3.org/TR/grddl/) XSLT is used to transform XML to RDF/XML, a concrete syntax of the early days of RDF still supported by most RDF tools, allowing the data to be read as RDF. The used XSLT document is part of the bundled gg2rdf GitHub action (https://github.com/plazi/gg2rdf) together with the other transformation steps required to generate a transformation result in the both human- and machine-readable RDF Turtle format. On the GitHub Actions page of the treatments-xml repository (https://github.com/plazi/treatments-xml/actions) one can see that every commit to this repository triggers a workflow run that takes approximately 12 minutes to execute. After that the transformation results are available in the treatments-rdf repository (https://github.com/plazi/treatments-rdf/). The commit of RDF data to the treatments-rdf repository triggers a webhook that loads the newly added data to the Plazi triplestore making it virtually immediately available in Synospecies.
biodiversity, RDF, knowledge graph, treatment, citation, ontology, SPARQL, TreatmentBank
Reto Gmür
TDWG 2022
The TreatmentBank infrastructure is supported by the Horizon Europe funded project Biodiversity Community Integrated Knowledge Library (BiCIKL), the Arcadia Fund and the Swissuniversities funded eBioDiv project.
BiCIKL https://bicikl-project.eu/ grant number 101007492
Arcadia Fund https://www.arcadiafund.org.uk/
Swissuniversities https://www.swissuniversities.ch/themen/digitalisierung/open-science-2021-2024
eBioDiv https://ebiodiv.org/