Don’t make me think Biodiversity data publishing made easy Vince Smith, Alice Heaton, Laurence Livermore, Simon Rycroft, Ben Scott & Lyubomir Penev* The.

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Presentation transcript:

Don’t make me think Biodiversity data publishing made easy Vince Smith, Alice Heaton, Laurence Livermore, Simon Rycroft, Ben Scott & Lyubomir Penev* The Natural History Museum London Pensoft Publishing*, Bulgaria

Data curation Data curation Data publishing Data publishing What we need is… Data collection & generation Data collection & generation a seamless workflow Data analysis 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 (

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) Projects Conservation RegionsSocieties Examples of Scratchpad use

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 publishing module

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) (Scratchpad project) (Developer resources) (Git repository) Scratchpad Publication Module (also GPLv2) HEAD:/sites/all/modules/custom/publication Biodiversity Data Journal 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)