Publishing Biodiversity:The interplay between Scratchpads and    the new Biodiversity Data Journal Koureas D.N.1, Rycroft ...
Our current taxonomic data production       •    15-20k new spp. described annually (2M total)1       •    30k nomenclatur...
The four nodes of data workflow1.   We collect and   generate data2.   We   curate, link and structure data3.   We   analy...
The four nodes of data workflowWhat are thebottlenecksin the workflow?                           Data                     ...
What we need is…aseamlessworkflow                     Data                              Data                         colle...
To achieve this…                                                This requires data, information & knowledge      Link toge...
ScratchpadsVirtual Research Environments      Making taxonomy digital, open & linked
so…what aretheScratchpads?
What are Scratchpads?• Hosted websites for biodiversity data• Virtual research & publication platform• Completely open acc...
What are Scratchpads?facilitatedevelopment of online research communitiesthroughstandardized environment of entering and c...
The Scratchpads conceptA Scratchpad is a website that holds data for you and your community  Your data                    ...
Examples of use:                                         Taxa(Classifications, taxon profiles, specimens, literature, imag...
Are Scratchpads sustainable?464 Scratchpads Communitiesby   6,407 active registered users                                 ...
Are Scratchpads sustainable?2007   2011                                   2014              ViBRANT              Virtual B...
the mainfeatures
The main featuresDynamic Biological Classifications                                     Manually entered or imported      ...
The main featuresTaxon pages              Overview of data related to taxon              Generated from tagged content
The main features         Bibliography managementAn inbuilt Bibliography managerFaceted browsingTaxon tagging and free key...
The main features        Specimen/Observation dataAnnotated full specimen/observation recordsLinked to images and georefer...
The main featuresDistribution maps                      Google maps based                      Data layers                ...
The main featuresCharacter matrices – Key construction             Quantitative or qualitative characters             Auto...
The main featuresMedia handling                   Bulk upload                   Metadata (incl. EXIF)                   Me...
The main featuresGeneration of custom pages                                 Tagged or not                                 ...
The main featuresEnhanced communication tools                                 Working groups                              ...
The main featuresanalyticaltoolsOBOE servicei.a.Ecological informatics,Phylogenetics,Sequence alignment
The main featuresdatamobilisation               more on the way…
The main featuresThePublicationmodule              Open-access                   journal
What will BDJ publish?• Single taxon treatments and  nomenclatural acts• Local or regional checklists• Sampling reports an...
How doScratchpadsandBDJinteract?
Working in a single environmentAllow submission ofdatasetsfor publicationwithoutreformatting and restructuring            ...
The publication moduleData included in manuscript in a structured annotated formatAuthor names and affiliations
The publication moduleTaxon descriptions
The publication moduleSpecimen data
The publication moduleAuthor names and affiliations          Taxon descriptions              Specimen data           Figur...
The data workflow                                                  XMLCommunity                                           ...
The editorial workflowScratchpads             Penso                               Peer-review op ons                      ...
Example papers via Scratchpads…Blagoderov V, Hippa H, Nel A (2010). ZooKeys 50: 79–90.       Faulwetter S, Chatzigeorgiou ...
AcknowledgementsScratchpads technical development - Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine BoutonScr...
Data                     Data                collection &                 collection &                generation          ...
Authors and Contributors                          Contributors           (mentor, linguis c editor, copy editor,          ...
Publishing biodiversity: The interplay between Scratchpads and the new Biodiversity Data Journal
Publishing biodiversity: The interplay between Scratchpads and the new Biodiversity Data Journal
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Publishing biodiversity: The interplay between Scratchpads and the new Biodiversity Data Journal

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Publishing biodiversity: The interplay between Scratchpads and the new Biodiversity Data Journal

  1. 1. Publishing Biodiversity:The interplay between Scratchpads and the new Biodiversity Data Journal Koureas D.N.1, Rycroft S. 1, Baker E. 1, Livermore L. 1, Scott B. 1, Heaton A.1, Bouton K.1, Penev L.2, Roberts D.1 and Smith V.S.1 1 The Natural History Museum London 2 Pensoft Publishers
  2. 2. Our current taxonomic data production • 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 Typically 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.
  3. 3. The four nodes of data workflow1. We collect and generate data2. We curate, link and structure data3. We analyse data4. We publish data
  4. 4. The four nodes of data workflowWhat are thebottlenecksin the workflow? Data Data collection & collection & generation generation bottleneck Data Data Data Data publishing publishing curation curation bottleneck Data Data analysis analysis
  5. 5. What we need is…aseamlessworkflow Data Data collection & collection & generation generation Data Data Data Data publishing publishing curation curation Data Data analysis analysis
  6. 6. To achieve this… This requires data, information & knowledge Link together “ to be… evolutionary •Digital data… by developing Not printed paper •Openly accessible analytical tools and Not behind barriers (e.g. paywalls) proper •Linked-up documentation and Not in silos then use this framework to conduct comparative analyses, studies of evolutionary process Global Systematics and biodiversity analyses”Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
  7. 7. ScratchpadsVirtual Research Environments Making taxonomy digital, open & linked
  8. 8. so…what aretheScratchpads?
  9. 9. What are Scratchpads?• Hosted websites for biodiversity data• Virtual research & publication platform• Completely open access & open source• Modular & flexible
  10. 10. What are Scratchpads?facilitatedevelopment of online research communitiesthroughstandardized environment of entering and curating datathat allowsharing and interlinkinganddissemination of research products
  11. 11. The Scratchpads conceptA Scratchpad is a website that holds data for you and your community Your data External data & services
  12. 12. Examples of use: Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
  13. 13. Are Scratchpads sustainable?464 Scratchpads Communitiesby 6,407 active registered users In total more thancovering 52,661 taxain 559,488 pages. 1,200,000 visitorsPer month unique visitors to Scratchpads sites 65000 unique visitors/month
  14. 14. Are Scratchpads sustainable?2007 2011 2014 ViBRANT Virtual Biodiversity Research & & Other grants in the pipeline Proposals?
  15. 15. the mainfeatures
  16. 16. The main featuresDynamic Biological Classifications Manually entered or imported Auto generated
  17. 17. The main featuresTaxon pages Overview of data related to taxon Generated from tagged content
  18. 18. The main features Bibliography managementAn inbuilt Bibliography managerFaceted browsingTaxon tagging and free keywordsImport from and export to all major formats
  19. 19. The main features Specimen/Observation dataAnnotated full specimen/observation recordsLinked to images and georeferenced
  20. 20. The main featuresDistribution maps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data
  21. 21. The main featuresCharacter matrices – Key construction Quantitative or qualitative characters Auto generation of keys Taxon based matrices [Specimens based character matrices]
  22. 22. The main featuresMedia handling Bulk upload Metadata (incl. EXIF) Media galleries
  23. 23. The main featuresGeneration of custom pages Tagged or not External RSS Twitter feeds Media files
  24. 24. The main featuresEnhanced communication tools Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments
  25. 25. The main featuresanalyticaltoolsOBOE servicei.a.Ecological informatics,Phylogenetics,Sequence alignment
  26. 26. The main featuresdatamobilisation more on the way…
  27. 27. The main featuresThePublicationmodule Open-access journal
  28. 28. 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 of species and communities?• Single identification keys• biodiversity-related databases, including genomic, ecological and environmental data (data papers)• Biodiversity-related software tools
  29. 29. How doScratchpadsandBDJinteract?
  30. 30. Working in a single environmentAllow submission ofdatasetsfor publicationwithoutreformatting and restructuring based on standardised XML schema
  31. 31. The publication moduleData included in manuscript in a structured annotated formatAuthor names and affiliations
  32. 32. The publication moduleTaxon descriptions
  33. 33. The publication moduleSpecimen data
  34. 34. The publication moduleAuthor names and affiliations Taxon descriptions Specimen data Figures and Tables XML XML Keys References Texts
  35. 35. The data workflow XMLCommunity submission PENSOFT JOURNAL SYSTEM SCRATCHPADS (PJS 2.0) MANUSCRIPT PUBLISHED MANUSCRIPT PUBLISHED (XML, PDF) (XML, PDF) Archive datasets Occurrence data Taxon treatments Taxon names Plazi Wiki
  36. 36. The editorial workflowScratchpads Penso Peer-review op ons Journal Public Community System Closed (PJS) Review Review Nominated reviewers requests Review Editor Collabora ve Panel reviewers online wri ng Online edi ng Review Editorial decision & feedback Public reviewers Authors Publica on & All reviews assembled into a Online edi ng dissemina on single online version Author’s revised manuscript
  37. 37. Example papers via Scratchpads…Blagoderov V, Hippa H, Nel A (2010). ZooKeys 50: 79–90. Faulwetter S, Chatzigeorgiou G, Galil BS, Nicolaidou A, Brake I, von Tschirnhaus M (2010). ZooKeys 50: 91–96. doi: 10.3897/zookeys.50.506 Arvanitidis C (2011. ZooKeys 150: 327–345. doi: doi: 10.3897/zookeys.50.505 10.3897/zookeys.150.1877http://sciaroidea.info/node/44428 http://polychaetes.marbigen.org/node/35 http://milichiidae.info/node/14995 Live (updated) versions of these papers
  38. 38. AcknowledgementsScratchpads 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 Reeve Pensoft - Lyobomir Penev and the teamOur 7000 users
  39. 39. Data Data collection & collection & generation generation Data Data Data Datapublishing publishing Thank you curation curation Data Data analysis analysis
  40. 40. Authors and Contributors Contributors (mentor, linguis c editor, copy editor, poten al reviewer, colleague/friend) Con trib u ng ite Inv Manuscript ready to submit Taxon treatment Template- based Interac ve key manuscript Checklist AuthoringLead author crea on Data paper Inv ite ing hor Aut Co-authors

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