Online direct import of specimen records from iDigBio infrastructure into taxonomic manuscripts
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The document discusses the online direct import of specimen records into taxonomic manuscripts using the ARPHA writing tool and IDigBio infrastructure. It highlights the benefits of importing data for error reduction, time savings, and improved data visibility while facilitating collaborative taxonomic publishing. The process enables the automatic export of data in various standards and formats, enhancing discoverability and opportunities for collaboration.
Online direct import of specimen records from iDigBio infrastructure into taxonomic manuscripts
- 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 [email protected] Pensoft & iDigBio Webinar, 16 June 2015
- 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. Data deluge: We now sample more data than we can digest (analyze, publish & use) Drawings: slavenapeneva.com
- 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. Step 1: Step 1: Start a taxonomic manuscript in ARPHA, and open a taxon treatment
- 7. Step 1: Step 2a: Click at the Materials section within the treatment
- 8. Step 2b: Three ways to import specimen occurrence records into a manuscript
- 9. Step 3: Import from iDigBio (or GBIF, or BOLD, or PlutoF) using record ID(s)
- 10. Where to take record IDs from iDigBio?
- 11. Where to take record IDs from iDigBio?
- 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. This is how data look like in the published paper
- 15. Easy export, harvesting & re-use
- 16. Live demo
- 17. Can we generate and import an entire manuscript?
- 18. Live demo
- 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 [email protected] For developers and data managers: Pensoft API
- 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
Editor's Notes
- #2: 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. Enjoy, Viktor
- #6: 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.