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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).
Citation preview
A paradigm shift in biodiversity publishing
The new Biodiversity Data Journal
E. Baker1, D.N Koureas1, L. Penev2
1 Natural History Museum, London2 Bulgarian Academy of Sciences & Pensoft Publishers, Sofia
Publications based on countless
specimens, images, maps, keys and datasets
Current taxonomic data production
Figure from Costello M.J et al, 2013. doi: 10.1126/science.1230318
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
Expected volume
of taxonomic and
biodiversity data
Need of extracting,
aggregating and linking
data on a global level
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
Data curation
Data publishing
The four nodes of data cycle
Data collection &generation
What are the
bottlenecks
in the workflow?
Data analysis
Lack of a wider conceptual frameLack of resources (incl. time)Time consuming workShifting to a new project
Investigator-focused
small data
dark data
20%
80%
Published and discoverable data
Dark data more important mainly due to their volume1
1Heidorn PB. Library Trends 57:280-299
Typically generated by
small communities or
individual researchers for “local” research projects
small data count!
Local floristic/faunistic studies
Singe nomenclatural acts
Small taxonomic treatments
Ecological and morphological datasets
Occurrence records
The building blocks of the world of biodiversity…
Publishing & Dissemination
impediment
Deprives the community of invaluable data
Mobilisationimpediment
Prevents researchers from taking credit for their work
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
?
!
Biodiversity Data Journal
• Open Access peer-review data
journal
• Structured, reusable,
standardized data
• Linked to Scratchpads via
Publication Module
http://biodiversitydatajournal.com/
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
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, …)
Choose article template
Assign classifications
Taxon Treatment
Manuscript Preview
Reuse of Data
Published ManuscriptPDF, HTML, XML
Articles Bibliographies Occurrences Taxon Treatments Taxon Names
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
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