A paradigm shift in biodiversity publishing
The new Biodiversity Data Journal

E. Baker1, D.N Koureas1, L. Penev2
1 Natura...
Current taxonomic data production

Publications based on countless

specimens, images, maps, ke
ys and datasets
Figure fro...
On the other hand:
Estimates of

7.5 million species
still undescribed1

1How

Many Species Are There on Earth and in the ...
Expected volume

Need of

of taxonomic and

extracting, aggregating

biodiversity data

and linking
level

data on a globa...
The four nodes of data cycle

1.

We collect and generate data

2.

We curate, link and structure data

3.

We analyse dat...
The four nodes of data cycle
What are the

bottlenecks
Data

in the workflow?

collection &
generation

Data
publishing

L...
Investigator-focused

Dark data more important
mainly due to their volume1

small data

Typically generated by

80%
dark d...
The building blocks of the world of biodiversity…
Local floristic/faunistic studies

Singe nomenclatural acts

Small taxon...
Publishing &
Dissemination
impediment

Mobilisation
impediment

Prevents researchers from
taking credit for their work

De...
The

BIG question

?

How do you incentivise researchers
to use tools that structure and open their data?

!

Enable them ...
Biodiversity Data Journal
• Open Access peer-review data
journal
• Structured, reusable, standardize
d data
• Linked to Sc...
What BDJ publish?
• Single taxon treatments and nomenclatural acts
• Local or regional checklists
• Sampling reports and o...
Speeding up: Pensoft Writing Tool
• Collaborative online editing
• Uses templates
• Identification key builder
• Assemble ...
Choose article template
Assign classifications
Taxon Treatment
Manuscript Preview
Reuse of Data

Published Manuscript
PDF, 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...
A paradigm shift in biodiversity publishing: Mobilization, mark up, reuse and integration of small data
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A paradigm shift in biodiversity publishing: Mobilization, mark up, reuse and integration of small data

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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).

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  • Με τις τελευταίες εκτιμήσεις να υπολογίζουν πως ακόμη έχουμε να περιγράψουμε 8 εκατ. είδη
  • Ο αριθμός των ταξινομικών και σχετικών με τη βιοποικιλότητα δεδομένων αναμένεται να αυξηθεί ραγδαία τα προσεχή χρόνια. Και παράλληλα η άύξηση αυτή συνοδεύεται από την ανάγκαιότητα να μπορούμε να τα ανασύρουμε, συναθροίσουμε και διασυνδέσουμε όχι σε τοπικό αλλά σε παγκόσμιο επίπεδο.
  • The Although data from 'data-rich' nations are being discovered at a snail's pace, there are no definite efforts being made to ensure discovery of data resources from mega-biodiverse, developing and under-developed regions of the world. Most of the existing data discovery efforts are geared towards big projects or initiatives that constitute less that 20% of the estimated universe of biodiversity data: the remaining 80% of the data, not easily found by potential user, is called 'dark data' [50]. These include investigator-focused 'small data', locally generated 'invisible data' and 'incidental data', which are less well planned, poorly curated and unlikely to be visible to others. These dark data are in danger of being lost for want of an appropriate discovery mechanism [51]. According to Heidorn (2008), these dark data may be more important, because of their huge volume, than the data that can be easily discovered and used [50].
  • The initial release of the module will allow you to publish in Pensoft’s new publication, the Biodiversity Data Journal.It is a new open-access data journal which will launch in mid-2013 and support the entire life-cycle of a manuscript from inception to publication.With the new Writing Tool, authors, co-authors and contributors can collaboratively work on a manscript before submitting it for review. Using the new Journal System, editors can easily manage the review process and authors can select to have a completely open review process where any member of the scientific community can comment on the paper during the review stage.Finally, once the paper is accepted and published, it is available as a PDF and in HTML and XML formats. It is widely disseminated to biodiversity data aggregators, services and archives.The BDJ is linked to Scratchpads via the new Publication Module which allows the submission of entire manuscripts from your Scratchpad!
  • The BDJ will publish a variety of articles and data including:Single taxon treatments and nomenclatural acts – accretional taxonomic workLocal, regional and habitat-based checklists and sampling reportsInteresting or novel ecological and biological observationsSingle free-standing identification keysAny kind of biodiversity-related databases and datasetsBiodiversity software tools and usecases
  • The BDJ will publish a variety of articles and data including:Single taxon treatments and nomenclatural acts – accretional taxonomic workLocal, regional and habitat-based checklists and sampling reportsInteresting or novel ecological and biological observationsSingle free-standing identification keysAny kind of biodiversity-related databases and datasetsBiodiversity software tools and usecases
  • The BDJ will publish a variety of articles and data including:Single taxon treatments and nomenclatural acts – accretional taxonomic workLocal, regional and habitat-based checklists and sampling reportsInteresting or novel ecological and biological observationsSingle free-standing identification keysAny kind of biodiversity-related databases and datasetsBiodiversity software tools and usecases
  • The BDJ will publish a variety of articles and data including:Single taxon treatments and nomenclatural acts – accretional taxonomic workLocal, regional and habitat-based checklists and sampling reportsInteresting or novel ecological and biological observationsSingle free-standing identification keysAny kind of biodiversity-related databases and datasetsBiodiversity software tools and usecases
  • The BDJ will publish a variety of articles and data including:Single taxon treatments and nomenclatural acts – accretional taxonomic workLocal, regional and habitat-based checklists and sampling reportsInteresting or novel ecological and biological observationsSingle free-standing identification keysAny kind of biodiversity-related databases and datasetsBiodiversity software tools and usecases
  • The BDJ will publish a variety of articles and data including:Single taxon treatments and nomenclatural acts – accretional taxonomic workLocal, regional and habitat-based checklists and sampling reportsInteresting or novel ecological and biological observationsSingle free-standing identification keysAny kind of biodiversity-related databases and datasetsBiodiversity software tools and usecases
  • The BDJ will publish a variety of articles and data including:Single taxon treatments and nomenclatural acts – accretional taxonomic workLocal, regional and habitat-based checklists and sampling reportsInteresting or novel ecological and biological observationsSingle free-standing identification keysAny kind of biodiversity-related databases and datasetsBiodiversity software tools and usecases
  • A paradigm shift in biodiversity publishing: Mobilization, mark up, reuse and integration of small data

    1. 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. 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. 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. 4. Expected volume Need of of taxonomic and extracting, aggregating biodiversity data and linking level data on a global
    5. 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. 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. 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. 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. 9. Publishing & Dissemination impediment Mobilisation impediment Prevents researchers from taking credit for their work Deprives the community of invaluable data
    10. 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. 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. 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. 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. 14. Choose article template
    15. 15. Assign classifications
    16. 16. Taxon Treatment
    17. 17. Manuscript Preview
    18. 18. Reuse of Data Published Manuscript PDF, HTML, XML Articles Bibliographies Occurrences Taxon Treatments Taxon Names
    19. 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

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