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 London Pensoft 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 , 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 a seamless 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? (

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 ProjectsRegionsSocieties

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 EOL Dryad GBIF Wiki Species-Id PubMed Plazi Select, describe & annotate data Publication 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

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

XML Figures 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) EOL Dryad GBIF PubMed Central and more... WRITING REVIEWING PUBLICATION

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