The Scratchpads platform is being developed for the last 5 years under this framework. To provide researchers with the necessary tools to make taxonomy digital, open and linked!To facilitate the development of virtual research environments
In the project there are more than 21 eMonocot Scratchpads which have over 45 international collaborating scientists.The eMonocot Scratchpads cover over 15 families with more planned with additional workshops which will take place this year at Monocots V in New York.The Scratchpad to eMonocot Portal link is now active and available for the public to browse all the Scratchpad data combined with other external monocot resources.
All of the information is brought together in the eMonocot portal. The information presented here will be especially useful for anyone studying the ecology or evolution of the monocot plants, or who wants to understand monocot biodiversity and conservation.The portal provides taxon descriptions, distribution maps, taxonomies and keys, all of which are downloadable and attributed to the author and contributing site.
Intuitive professional looking layout.Easy to compile taxon pages without any knowledge of web design.Taxonomy provides the crucial backbone, linking content together and is easily updateable.On this page you can see the classification browser in the side bar, detailed nomenclatural information, images and a diagnostic summary.
Prior to submission all data are validated to ensure there are no important missing fields.Once you have finished your manuscript there is a simple one-click submission process where all your specified authors and contributors are given access to the article in the Pensoft Journal System and will be updated on the review process.
Scratchpads introductory presentation 45mins
ScratchpadsVirtual Research Environmentsfor taxonomic and biodiversity related data
Scratchpads introductory presentation. DimitriosKoureas, Laurence Livermore. figshare. 2013.doi:10.6084/m9.figshare.640101Where to find and how to cite this presentation
Publications based on countlessspecimens, images, maps, keys and datasetsCurrent taxonomic data productionTypically generated bysmall communitiesfor “local” research projectsFigure from Costello M.J et al, 2013. doi: 10.1126/science.1230318
On the other hand:Estimates of7.5 million speciesstill undescribed11How Many Species Are There on Earth and in the Ocean? Mora C et al.doi:10.1371/journal.pbio.1001127
Expected volumeof taxonomic andbiodiversity dataNeed ofextracting, aggregatingand linking data on a globallevel
The four nodes of data workflow1.We collect and generate data2.We curate, link and structure data3.We analyse data4.We publish data
DatacurationDataanalysisDatapublishingThe four nodes of data workflowDatacollection &generationWhat are thebottlenecksin the workflow?
DatacurationDataanalysisDatapublishingWhat we need is…Datacollection &generationaseamlessworkflow
Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001This requires data, information & knowledgeto be…• DigitalNot printed paper• Openly accessibleNot behind barriers (e.g. paywalls)• Linked-upNot in silos“Link togetherevolutionarydata… by developinganalytical tools andproperdocumentation andthen use this framework toconduct comparativeanalyses, studies ofevolutionary process andbiodiversity analyses”To achieve this…
ScratchpadsVirtual Research EnvironmentsMaking taxonomy digital, open & linked
What are Scratchpads?• Hosted websites for biodiversity data• Virtual research & publication platform• Completely open access & open source• Modular & flexible
What are Scratchpads?development of online research communitiesfacilitatestandardized environment of entering and curating datathroughsharing and interlinkingthat allowdissemination of research productsand
A Scratchpad is a website that holds data for you and your communityThe Scratchpads conceptYour data External data & services
Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic& morphometric datasets, keys, phylogenies)ProjectsConservation Regions SocietiesExamples of use:
Red List conservation assessmentsExamples of use:
Examples of use:Bulbous monocot genera listed in CITES
Global Invasive Alien Species Information PartnershipExamples of use:
Major integrated projects• Online resource formonocot plants• Collaboration betweenKew, Oxford Universityand NHM• Data to be open andusable by other scientists
Major integrated projects• 21+ open community sites andgrowing• Over 45 internationallycollaborating scientists• Site data feeds into a “Portal”Site List: http://about.e-monocot.org/list-emonocot-scratchpads
Major integrated projects• Retrieve information onany Monocot plant• Rich downloadable data• Identification keys• Model example of linkedattributed dataeMonocot Portal: http://e-monocot.org/
65,000unique visitors/monthPer month unique visitors to Scratchpads sites580Scratchpads Communitiesby 8,185active registered userscovering 155,607taxain 653,274 pages.Are Scratchpads sustainable?In total more than1,200,000 visitors
Are Scratchpads sustainable?2007 2011 2014ViBRANTVirtual Biodiversity Research& &Other grants in the pipelineProposals?
Submission & enhanced peer review• Manuscript data validation• One-click submission to BDJ• Traditional peer review and optional panel/public review
XMLFigures and TablesKeysReferencesTextsThe publication moduleAuthor names and affiliationsTaxon descriptionsSpecimen data
The data workflowMANUSCRIPT PUBLISHED(XML, PDF)PENSOFT JOURNAL SYSTEM(PJS 2.0)XMLsubmissionSCRATCHPADSCommunityTaxon namesOccurrence datadatasetsArchive Taxon treatmentsPlazi Wiki
What will BDJ publish?• Single taxon treatments andnomenclatural acts• Local or regional checklists• Sampling reports and occasionalinventories• Habitat-based checklists and inventories• Ecological and biological observations ofspecies and communities?• Single identification keys• biodiversity-related databases, includinggenomic, ecological and environmentaldata (data papers)• Biodiversity-related software tools
Scratchpads are an integrated system toEnter, Curate, Mark-up, Link and Publish datataxonomic workflowin a single virtual environment
Scratchpads technical development- Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine BoutonScratchpads outreach- Laurence Livermore, Isa van deVelde & Dimitris Kourease-Monocot- Paul Wilkin & the Kew team, Charles Godfray & the Oxford teamViBRANT- Vince Smith, Dave Roberts & Lucy ReevePensoft- Lyobomir Penev and the Pensoft teamOur 8000 usersAcknowledgements
Help & Support• In-site Support• Wiki• Training Courses (12 in 2012)• Ambassadors Programme• Embedded Issues Queue• Sandbox Sitehttp://help.scratchpad.eu
Authors and ContributorsLead authorContributors(mentor, linguis c editor, copy editor,poten al reviewer, colleague/friend)Co-authorsInviteInviteTemplate-basedmanuscriptcrea onTaxon treatmentInterac ve keyChecklistData paperAuthoringAuthoringContribungManuscript ready to submit
• 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 datasetsOur current taxonomic data productionTypically generated by small communities for“local” research projectsFigures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.