Don’t make me thinkBiodiversity data publishing made easy

Vince Smith, Alice Heaton, Laurence Livermore, Simon Rycroft, Ben Scott & Lyubomir Penev*

The Natural History Museum LondonPensoft Publishing*, Bulgaria

Data curation

Data publishing

What we need is…

Data collection &generation

aseamless

workflow

Data analysis

• Hosted websites for biodiversity data

• Virtual research environments

• Completely open access & open source

• Modular & flexible• Running since 2007• Making taxonomy

digital, open & linked

Scratchpads (http://Scratchpads.eu)

65,000 unique visitors/month

Per month unique visitors to Scratchpad sites

512 Scratchpad Communities

by 6,500 active registered users

covering 73,444 taxa

in 515,189 pages.

Scratchpad usage metrics

81 paper citations in 2012

In total more than

1,300,000 visitors

Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic

& morphometric datasets, keys, phylogenies)

ProjectsConservation Regions Societies

Examples of Scratchpad use

Data curation

Data publishing via Scratchpads

Data collection &generation

Data analysis

Data publishing

No kudos, credit

or citation of data in Scratchpads

Structured data

Publish, cite,disseminate & archive data

EOLDryad GBIFWiki Species-IdPubMed Plazi

Select, describe &

annotate dataPublication module

Biodiversity Data Journal

• New, Open Access data journal• Launches Mid-2013• Supports the full life cycle of a

manuscript• Writing, submission, review,

publication & dissemination• Structured, reusable,

standardized data• Linked to Scratchpads via

publishing modulehttp://biodiversitydatajournal.com/

The publication module

Scratchpad templates for publishing...• Taxon treatments• Nomenclatural acts • Checklists / inventories• Identification keys and trees• Metadata descriptions of databases• Descriptions of software tools

Easy & intuitive• Draws on data from your site• Pre-submission validation• Submitted as structured XML• No reformatting

Assembling a manuscript

1. Add article level metadata...• Choose authors, select template• Add context (title, abstract)

2. Select data• Taxon descriptions• Specimens• Datasets• Figures & tables• Keys & trees

3. Describe data• Intro., methods, conclusions• Auto-compile references

4. Submit• Preview manuscript• Validate

After submission

More information

Scratchpads (GPLv2 License)• http://scratchpads.eu/ (Scratchpad project)• http://scratchpads.eu/develop/repository (Developer resources)• https://git.scratchpads.eu/v/scratchpads-2.0.git/tree (Git repository)

Scratchpad Publication Module (also GPLv2)• https://git.scratchpads.eu/v/scratchpads-2.0.git/tree/

HEAD:/sites/all/modules/custom/publication

Biodiversity Data Journal• http://biodiversitydatajournal.com/

Credits• Alice Heaton, Simon Rycroft, Ben Scott (programming)• Laurence Livermore (user testing & support)• Lyubomir Penev & the Pensoft team (Biodiversity Data Journal)

Funding• EU FP7 Infrastrastructures (ViBRANT), UK NERC (e-Monocot)