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Scratchpads Publication Module. - A paradigm shift in publishing. RBG Kew, Seminar, 17-04-2013. Our current taxonomic data production. 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 - PowerPoint PPT Presentation
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Scratchpads Publication Module
- A paradigm shift in publishing
RBG Kew, Seminar, 17-04-2013
• 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.
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 workflow
1. We collect and generate data
2. We curate, link and structure data
3. We analyse data
4. We publish data
Data curation
Data analysis
Data publishing
The four nodes of data workflow
Data collection &generation
What are the
bottlenecks
in the workflow?
Data curation
Data analysis
Data publishing
What we need is…
Data collection &generation
aseamless
workflow
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…
ScratchpadsVirtual Research Environments
Making taxonomy digital, open & linked
What are Scratchpads?
Hosted websites for biodiversity data
Virtual research & publication platform
Completely open access & open source
Modular & flexible
The
Publication module
Open-accessjournal
The main features
How do
Scratchpads and
BDJ interact?
Allow submission of datasets for publication without reformatting and restructuring
Working in a single environment
based on standardised XML schema
Assembling a manuscript
XMLFigures and Tables
References
Manuscript text
Submitting your data
Author names and affiliations
Taxon descriptions
Specimen data
Previewing your manuscript
Submission & enhanced peer review
• Manuscript data validation
• One-click submission to BDJ
• Traditional peer review and optional panel/public review
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
The data workflow
MANUSCRIPT PUBLISHED(XML, PDF)
PENSOFT JOURNAL SYSTEM (PJS 2.0)
XML submission
SCRATCHPADS
Com
mun
ity
Taxon namesOccurrence datadatasetsArchive Taxon treatments
Plazi Wiki
Upcoming features
• Additional manuscript types (checklists, keys & data)
• Post-publication Scratchpad data feedback
• Publish directly in Phytokeys, Zookeys etc
Scratchpads are an integrated system to
Enter, Curate, Mark-up, Link and Publish data
taxonomic workflowin a single virtual environment
Launch Date:
May 2013
Currently accepting manuscripts from Scratchpads or
via the online Pensoft Writing Tool