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).

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. 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

5. REPOSITORIES
ARPHA WRITING TOOL
MANUSCRIPT
PULISHED ARTICLE

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

14. Mapping & visualization

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
info@pensoft.net
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

21. I Open Science!
PLAZI