One of the major flaws of conventional publishing of biodiversity research is the generally low accessibility and reuse of the published information and data. The continuing practice of publishing in non-machine-readable formats, such as paper and PDF, is one of the five causes of the “Publishing bottleneck”, a phenomenon comparable to the “taxonomic impediment” in biodiversity research. Further motivation for shifting the current model in scholarly publishing is the growing demand from funders for open access to data combined with the rapidly increasing amount of data due to the intensification of methods for scientific exploration, e.g. genome sequencing, large-scale inventories and accumulation of ecological data, low uptake and inconsistent policies for data publishing, pressure of funders and administrators to publish in “high-impact” journals, and increasing difficulties with peer-review, due to rising volume of publications and increasing time-pressure on reviewers. The new paradigm in modern digital publishing is to remove the restrictions of the print/PDF age and opening data that underpin research and make it easily available for re-use. The Biodiversity Data Journal (BDJ) (www.pensoft.net/journals/bdj) and associated Pensoft Writing Tool (PWT) (www.pwt.pensoft.net) launched within the EU-funded project ViBRANT (www.vbrant.eu) provide the first e-infrastructure and work flow ever to complete the full publishing life cycle within a single, fully XML-based, online collaborative platform. BDJ publishes papers in all scientific disciplines of biodiversity science. To increase the quality of published research text and data submitted to BDJ will be peer-reviewed by the scientific community through a novel community-based pre-publication peer-review and possibilities to comment after publication (post-publication peer-review).

1. A paradigm shift in biodiversity publishing
The new Biodiversity Data Journal
E. Baker1, D.N Koureas1, L. Penev2
1 Natural
History Museum, London
2 Bulgarian Academy of Sciences & Pensoft Publishers, Sofia

2. Current taxonomic data production
Publications based on countless
specimens, images, maps, ke
ys and datasets
Figure from Costello M.J et al, 2013. doi: 10.1126/science.1230318

3. On the other hand:
Estimates of
7.5 million species
still undescribed1
1How
Many Species Are There on Earth and in the Ocean? Mora C et al.
doi:10.1371/journal.pbio.1001127

4. Expected volume
Need of
of taxonomic and
extracting, aggregating
biodiversity data
and linking
level
data on a global

5. The four nodes of data cycle
1.
We collect and generate data
2.
We curate, link and structure data
3.
We analyse data
4.
We publish data

6. The four nodes of data cycle
What are the
bottlenecks
Data
in the workflow?
collection &
generation
Data
publishing
Lack of a wider conceptual frame
Lack of resources (incl. time)
Time consuming work
Shifting to a new project
Data
curation
Data
analysis

7. Investigator-focused
Dark data more important
mainly due to their volume1
small data
Typically generated by
80%
dark data
small communities
or
individual researchers
for “local” research projects
Published and
discoverable data
20%
1Heidorn
PB. Library Trends
57:280-299

8. The building blocks of the world of biodiversity…
Local floristic/faunistic studies
Singe nomenclatural acts
Small taxonomic treatments
Ecological and morphological datasets
Occurrence records
small data count!

9. Publishing &
Dissemination
impediment
Mobilisation
impediment
Prevents researchers from
taking credit for their work
Deprives the community
of invaluable data

10. The
BIG question
?
How do you incentivise researchers
to use tools that structure and open their data?
!
Enable them to take credit for ALL their work

11. Biodiversity Data Journal
• Open Access peer-review data
journal
• Structured, reusable, standardize
d data
• Linked to Scratchpads via
Publication Module
http://biodiversitydatajournal.com/

12. What BDJ publish?
• Single taxon treatments and nomenclatural acts
• Local or regional checklists
• Sampling reports and occasional inventories
• Habitat-based checklists and inventories
• Ecological and biological observations
• Single identification keys
• Biodiversity-related databases, including genomic, ecological
and environmental data (data papers)
• Biodiversity-related software tools & software documentation

13. Speeding up: Pensoft Writing Tool
• Collaborative online editing
• Uses templates
• Identification key builder
• Assemble plates from single figures
• Import specimens (DwC-A)
• Import references (CrossRef, PubMed, …)

14. Choose article template

15. Assign classifications

16. Taxon Treatment

17. Manuscript Preview

18. Reuse of Data
Published Manuscript
PDF, HTML, XML
Articles
Bibliographies
Occurrences
Taxon
Treatments
Taxon Names

19. Publish or perish?
Biodiversity informatics tools and e-infrastructures can be used to
take credit for our work
and
gain greater exposure for our data