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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A paradigm shift in biodiversity publishing: Mobilization, mark up, reuse and integration of small data
- 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, …)
- 16. Taxon Treatment
- 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
Editor's Notes
- 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