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pro-iBiosphere project demonstrates its pilots at the final conference in Meise (Brussels)
The pro-iBiosphere Final Event will take place on 9 – 13 June 2014 at the Bouchout Castle of the Botanic Garden Meise, Brussels. During the third day of the meeting a special event is designated for the demonstration of the pro-iBiosphere pilots.
During this session, the task and pilot leaders will demonstrate the tools and workflows developed or improved in the course of the project. The demonstration will be interactive and will allow for discussions, real-time tests and consultations on possible implementations by the interested stakeholders. The pilots and demos planned until now are:
Interoperability of taxon treatments
In the past, taxonomic information has been published in numerous scattered outlets and in different formats. The production of a taxonomic revision or such as a flora or fauna required that the appropriate text was discovered, and retyped manually. The current pilot demonstrates a greatly accelerated workflow that takes advantage of the informatics developments of pro-iBiosphere. The workflow locates, identifies, and enhances data included in treatments from both legacy and newly published taxonomic literature, facilitating discovery, analysis, and reuse through the Plazi Treatment Repository (PTR).
The workflow includes the following steps:
  • Step 1: Convert printed taxonomic articles/monographs to digital text format.
  • Step 2a: Mark up generic document features and domain-specific information (taxon treatments) and store the results at Plazi; and also
  • Step 2b: Export of newly published treatments marked up during the editorial process (for example in the journals ZooKeys, PhytoKeys and Mycokeys)
  • Step 3: Browse, search, export and re-use treatments coming from different sources.
Streamlining automated registration of taxon names between publishers and registries
The pre-publication registration of taxonomic and nomenclatural acts with registries such as the International Plat Name Index (IPNI), Index Fungorum, MycoBank, and ZooBank involves two main classes of actors: (1) publishers, and (2) registry curators. The publisher takes the responsibility for initiating the registration of nomenclatural acts so that the workflow can be performed following a common stepwise model:
  • Step 1. XML message from the publisher to the registry on acceptance of the manuscript containing the type of act, taxon names, and preliminary bibliographic metadata; the registry will store the data but not make these publicly available before the final publication date.
  • Step 2a. Response XML report containing the unique identified of the act as supplied by the registry and/or any relevant error messages.
  • Step 2b. Error correction and d-duplication performed manually: human intervention at either registry’s or publisher’s side (or at both).
  • Step 3. Inclusion of registry supplied identifiers in the published treatments (protologues, nomenclatural acts).
  • Step 4. Making the information in the registry publicly accessible upon publication, providing a link from the registry record to the artice.
Improved cooperation and interoperability of e-infrastructures
Challenges related to the technical interoperability of biodiversity data present themselves in competing standards, ambiguous, poor or absent documentation, lack of stable identifier systems and the absence of semantic interoperability. For improving the interoperability between e-infrastructures, stable identifiers for biodiversity collection objects and a global service registry were identified as the two major achievables for progress. The use of state-of-the-art digitisation software & tools for literature markup is another important factor.
  • Steps forward 1: Implementation of HTTP-URIs by 8 major institutions for their collection objects by October 2013 and recommendations for further topics to be explored in detail.
  • Steps forward 2: Agreement on the BiodiversityCatalogue as a global registry for biodiversity related services. Improvement recommendations for it to be able to fill this role even better, registration of services available now.
  • Steps forward 3: Workflow improvement between the Plazi document registry and the Common Data Model (CDM)-based EDIT Platform for Cybertaxonomy ( ). In the course of this a markup granularity table evolved. The pro-iBiosphere pilot portals visualize the data results at different stages and show the possibilities for scientists willing to mark up their data. The markup granularity table explains in detail work load and connected output gain.

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This project has received funding from the European Union’s Seventh Programme for research, technological development and demonstration under grant agreement No 312848