Don’t make me think Biodiversity Data Publishing Made Easy

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

The Natural History Museum LondonPensoft Publishing*, Bulgaria

• 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.

Data curation

Data curation

Data Publication

Data Publication

Data Collection &Generation

Data Collection &Generation

aseamless

workflow

Data Analysis

Data Analysis

The data cycle

• Hosted websites for

biodiversity data• Virtual research

environments• Completely open access

& open source• Modular & flexible• Running since 2007• Making taxonomy

digital, open & linked

What are Scratchpads? (http://scratchpads.eu)

65,000 unique visitors/month

Per month unique visitors to Scratchpad sites

525 Scratchpad Communities

by 6,550 active registered users

covering 73,444 taxa

in 535,317 pages.

Scratchpad usage metrics (July 2013)

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)

Examples of Scratchpad use

Conservation Projects Regions Societies

Data curation

Data curation

Data publishing via Scratchpads

Data collection &generation

Data collection &generation

Data analysis

Data analysis

Data publishing

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 modulePublication 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 Publication

Module http://biodiversitydatajournal.com/

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

• Single identification keys

• Biodiversity-related databases, including genomic, ecological

and environmental data (data papers)

• Biodiversity-related software tools

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

Scratchpads Publication Module

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

• Work on multiple manuscripts

• Invite different people to work on different manuscripts

• Manage permissions

Assembling a manuscript

Author names and affiliations

Data included in manuscript in a structured, annotated format

Assembling a manuscript

Taxon descriptions

Assembling a manuscript

Specimen data

Assembling a manuscript

References

Easily cite from your Scratchpad bibliography to compile a list of references

Assembling a manuscript

Figures

Assembling a manuscript

Tables

Assembling a manuscript

Texts

Assembling a manuscript

XMLXMLFigures and Tables

Keys

References

Text

The publication module

Author names and affiliations

Taxon descriptions

Specimen data

Supplementary files

Structured Data from your Scratchpad

Previewing your manuscript

After submission (summary)

EOLDryadGBIFPubMed Central

and more . . .

The Future…

Later in 2013 Pensoft and Scratchpads will support publication in other journals:

eMonocot Phytokeys Special Issue

• Invitation to stress test the new module!

• Special issue published in Phytokeys – Late 2013

• All manuscripts submitted via Scratchpads or PWT

• Technical and taxonomic data papers are welcome

• No page costs

Acknowledgements

Scratchpads technical development

- Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton, Katherine Bouton & Khalid Almaini

Scratchpads support & outreach

- Dimitris Koureas, Isa van de Velde, Laurence Livermore

ViBRANT

- Vince Smith, Dave Roberts & Lucy Reeve

Pensoft

- Lyobomir Penev and the Pensoft team

e-Monocot

- Paul Wilkin & the Kew team, Charles Godfray & the Oxford team

Our 6,500 users