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Online direct import of specimen records from iDigBio infrastructure into taxonomic manuscripts



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On 16 June 2016, V. Senderov and L. Penev held a webinar presenting two novel workflows developed at Pensoft Publishers and used in the Biodiversity Data Journal; (1) automatic import of specimen records into manuscripts, and (2) automatic generation of data paper manuscripts from Ecologocal Metadata Language (EML) metadata. The aim of the webinar was to familiarize the public with the workflows, and motivate them from a scientific standpoint. The title of the webinar was: "Online direct import of specimen records from iDigBio infrastructure into taxonomic manuscripts."

Integrated Digitized Biocollections (iDigBio) is the leading US-based aggregator of biocollections data. They hold regular webinars and workshops aimed at improving biodiversity informatics knowledge, which are attended by collection managers, scientists, and IT personnel. Thus, making a presentation for them was an excellent way of making our research and tools-development efforts widely known and getting feedback from the community.

Our efforts, which are part of the larger PhD project of V. Senderov to build an Open Biodiversity Knowledge Management System (OBKMS) (Senderov and Penev 2016), focused on two areas: optimizing the workflow of specimen or occurrence data and optimizing the workflow of dataset metadata. The results of these efforts are that now it is possible to directly import specimen or occurrence record information from GBIF, BOLD Systems, iDigBio, or PlutoF into ARPHA via a record identifier. No manual copying or retyping is required. Moreover, it is possible to generate a data paper manuscript from recent Ecological Metadata Langauge (EML) versions in ARPHA. The data paper concept is discussed throughly in Chavan and Penev (2011).

Online direct import of specimen records from iDigBio infrastructure into taxonomic manuscripts

  1. 1. Online direct import of specimen records from iDigBio infrastructure into taxonomic manuscripts Lyubomir Penev , Viktor Senderov Institute for Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria & Pensoft Publishers penev@pensoft.net Pensoft & iDigBio Webinar, 16 June 2015
  2. 2. Poll results 0 1 2 3 4 5 6 Librarian or data manager Student or scientist in biology Data or computer scientist IT specialist, database admin Other Please select what best describes you
  3. 3. Data deluge: We now sample more data than we can digest (analyze, publish & use) Drawings: slavenapeneva.com
  4. 4. Data import Authoring Peer-review Publication Dissemination + Next-Gen taxonomy requires Next-Gen publishing All within a single online collaborative platform! ARPHA Writing Tool & Biodiversity Data Journal facilitate data publishing & re-use
  6. 6. Step 1: Step 1: Start a taxonomic manuscript in ARPHA, and open a taxon treatment
  7. 7. Step 1: Step 2a: Click at the Materials section within the treatment
  8. 8. Step 2b: Three ways to import specimen occurrence records into a manuscript
  9. 9. Step 3: Import from iDigBio (or GBIF, or BOLD, or PlutoF) using record ID(s)
  10. 10. Where to take record IDs from iDigBio?
  11. 11. Where to take record IDs from iDigBio?
  12. 12. WHY import & publish specimen records in this way? Avoid re-typing errors and save time Tracking (provenance) information is saved in occurrenceDetails Mobilization, peer-review and publication of small data Data downloadable anytime as CSV file Machine-readable and harvestable (from the XML version of the published article) Automatically exported in Darwin Core Archive Automatically exported to and indexed by GBIF on the day of the publication Interoperable in DarwinCore standard Re-usable (new opportunities for collaboration) Increase discoverability, visibility, and citation of authors’ work
  13. 13. This is how data look like in the published paper
  14. 14. Mapping & visualization
  15. 15. Easy export, harvesting & re-use
  16. 16. Live demo
  17. 17. Can we generate and import an entire manuscript?
  18. 18. Live demo
  19. 19. http://arpha.pensoft.net/dev/ Allows to import different types of manuscripts from XML. E.g.: • Software Description • Taxonomic Paper • Data paper For collaborations please contact us at info@pensoft.net For developers and data managers: Pensoft API
  20. 20. Pensoft developers team European Commission: EUBON FP7 Project European Commission: PhD Financed through the EU Marie-Sklodovska-Curie Program Grant Agreement Nr. 642241 Slavena Peneva (drawings and design) Our sincere thanks are due to
  21. 21. I Open Science! PLAZI


  • Hello,

    If you wish to view the video recording of the live presentation, please visit http://idigbio.adobeconnect.com/p7sg0aym3e3/. More information from iDigBio can be found at the webinar information page.

  • This fictionalized workflow presents the flow of information content about biodiversity specimens or biodiversity occurrences from the data portals GBIF, BOLD Systems, iDigBio, and PlutoF, through user-interface elements in ARPHA to textualized content in a research manuscript in Biodiversity Data Journal.

    In the next few slides, we illustrate the workflow using the example of iDigBio.
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