Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Biodiversity Informa...arrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Biodiversity Information Science and Standards
Article . 2020 . Peer-reviewed
License: CC BY
Data sources: Crossref
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Article . 2020
License: CC BY
Data sources: ZENODO
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Pensoft
Conference object . 2020
Data sources: Pensoft
versions View all 3 versions
addClaim

Liberating the Richness of Facts implicit in taxonomic Publication: The Plazi Workflow 

Authors: Donat Agosti; Marcus Guidoti; Guido Sautter;

Liberating the Richness of Facts implicit in taxonomic Publication: The Plazi Workflow 

Abstract

The growing corpus of hundreds of millions of pages of taxonomic literature reporting research results based on specimens is very rich in facts. In order to make them reusable, Plazi, Pensoft and Zenodo are building and maintaining the Biodiversity Literature Repository which includes a workflow to discover, describe, store, in order to making these facts open access, findable, accesible, interoperable and reusable (FAIR). Currently, 43,000 articles have 406,000 material citations, and around 50% of annually new described species are made accessible and immediately reused by the Global Biodiversity Information Facility (GBIF). All the images are deposited at the Biodiversity Literature Repository (BLR), as well as the taxonomic treatments. For each of these deposits enriched metadata is added and a Digital Object Identifier (DOI) is minted. Through this process, Plazi is the single largest data set provider to GBIF and continues to provide ca. 45,000 unique taxonomic names at GBIF. The workflow is optimized for born digital portable data format (PDF) based publications, but other formats can also be ingested, including TaxPub, a taxonomy specific version of the Journal Article Tag Suit (JATS) XML. After ingestion, the PDF is readily converted to an open-access, proprietary format called Image Markup File (IMF). IMF is a compressed file format that consists of the enhanced information contained in the PDF, with figures and tables properly extracted. The IMFs are then housed at TreatmentBank, with associated exported files, including DwC-A for each parent article and their respective taxonomic treatments, XMLs of treatments and GBIF datasets of their parent articles. Taxonomic treatments, in addition to figures and the original PDFs, are also deposited on Zenodo, where a DOI is minted if none is already available. These Zenodo deposits include in the metadata links back to the different data and file formats, including the treatments XMLs, maintaining the system connected and up-to-date. Third-party players, like GBIF, Global Biotic Interactions (GloBI), Ocellus, OpenBiodiv and Synospecies are constantly fed by system hookups, which guarantees data consistency after further edits. The PDF-IMF conversion and data enhancement is possible due to Plazi’s open-source software called GoldenGate Imagine. Ingested XMLs, that are validated against the TaxPub scheme, follow a similar path into the system and the many third-party applications. This operation is supported by the Arcadia Fund as well by service contracts from publishers to disseminate their data. In addition, the workflow has been contributing treatments, images from numerous publications relevant to understanding the virus spillover as part of the CETAF COVID19 task force. In this lecture this workflow is described and explained, including the associated infrastructure and its ongoing changes and upcoming steps of development.

Keywords

open access, FAIR data, digital library, biodiversity

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
    OpenAIRE UsageCounts
    Usage byUsageCounts
    visibility views 3
    download downloads 6
  • 3
    views
    6
    downloads
    Powered byOpenAIRE UsageCounts
Powered by OpenAIRE graph
Found an issue? Give us feedback
visibility
download
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
views
OpenAIRE UsageCountsViews provided by UsageCounts
downloads
OpenAIRE UsageCountsDownloads provided by UsageCounts
0
Average
Average
Average
3
6
Green
gold
Related to Research communities
Italian National Biodiversity Future Center