scratchpads publication module - a paradigm shift in publishing rbg kew, seminar, 17-04-2013
TRANSCRIPT
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Scratchpads Publication Module
- A paradigm shift in publishing
RBG Kew, Seminar, 17-04-2013
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• 15-20k new spp. described annually (2M total)1
• 30k nomenclatural acts (12M total) 1
• 20k phylogenies (750k total)2
• 31k taxa sequenced (360k taxa total)3
• 800k BioMed papers (40M total pp. of taxonomy) 4
• Countless specimens, images, maps, keys and datasets
Our current taxonomic data production
Typically generated by small communities for “local” research projects
Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.
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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
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Expected volume
of taxonomic and
biodiversity data
Need of extracting,
aggregating and linking
data on a global level
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The four nodes of data workflow
1. We collect and generate data
2. We curate, link and structure data
3. We analyse data
4. We publish data
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Data curation
Data analysis
Data publishing
The four nodes of data workflow
Data collection &generation
What are the
bottlenecks
in the workflow?
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Data curation
Data analysis
Data publishing
What we need is…
Data collection &generation
aseamless
workflow
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Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
This requires data, information & knowledge to be…
• Digital Not printed paper
• Openly accessible Not behind barriers (e.g. paywalls)
• Linked-up Not in silos
“Link together evolutionary data… by developing
analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses”
To achieve this…
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ScratchpadsVirtual Research Environments
Making taxonomy digital, open & linked
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What are Scratchpads?
Hosted websites for biodiversity data
Virtual research & publication platform
Completely open access & open source
Modular & flexible
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The
Publication module
Open-accessjournal
The main features
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How do
Scratchpads and
BDJ interact?
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Allow submission of
datasets for publication
without reformatting and restructuring
Working in a single environment
based on standardised XML schema
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Assembling a manuscript
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XMLFigures and Tables
References
Manuscript text
Submitting your data
Author names and affiliations
Taxon descriptions
Specimen data
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Previewing your manuscript
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Submission & enhanced peer review
• Manuscript data validation
• One-click submission to BDJ
• Traditional peer review and optional panel/public review
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What will 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 of
species and communities?• Single identification keys • biodiversity-related databases, including
genomic, ecological and environmental data (data papers)
• Biodiversity-related software tools
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The data workfl ow
MANUSCRIPT PUBLISHED(XML, PDF)
PENSOFT JOURNAL SYSTEM (PJS 2.0)
XML submission
SCRATCHPADS
Com
mun
ity
Taxon namesOccurrence datadatasetsArchive Taxon treatments
Plazi Wiki
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Upcoming features
• Additional manuscript types (checklists, keys & data)
• Post-publication Scratchpad data feedback
• Publish directly in Phytokeys, Zookeys etc
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Scratchpads are an integrated system to
Enter, Curate, Mark-up, Link and Publish data
taxonomic workflowin a single virtual environment
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Launch Date:
May 2013
Currently accepting manuscripts from Scratchpads or
via the online Pensoft Writing Tool
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