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