Making your data work for you: Scratchpads, publishing & the Biodiversity Data Journal


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Vince Smith, Dave Roberts & Lyubomir Penev. Presented at the Linnean Society on 20th Sept. 2012.

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Making your data work for you: Scratchpads, publishing & the Biodiversity Data Journal

  1. 1. Making your data work for you: Scratchpads, publishing & the Biodiversity Data JournalLinnean Society, UK Vince Smith1, Dave Roberts1 & Lyubomir Penev220 September, 2012 1. Natural History Museum, London 2. Pensoft Publishers, Sofia, Bulgaria
  2. 2. Our informatics grand challenge… “Link together evolutionary data… by developing analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses” Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
  3. 3. Our informatics grand challenge… “Link together evolutionary This requires data, information data… by developing & knowledge to be… analytical tools and proper documentation and then • Digital use this framework to Not printed paper conduct comparative • Openly accessible analyses, studies of evolutionary process and Not behind barriers biodiversity analyses” • Linked-up Not in silos Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
  4. 4. Most of our output is not digital, open or linked • 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… 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.
  5. 5. ScratchpadVirtual Research Environments Making taxonomy digital, open & linked
  6. 6. What is a Scratchpad? A website for you & your community 1 2 3 Your data Uploaded & “Published” & reviewed tagged on your site Fast Intuitive Fit for use
  7. 7. Scratchpads • EDIT (07-11), ViBRANT / eMonocot (11-13) • Hosted websites for taxonomists • Taxonomic, regional or societal • Research & publication platform • Supports the taxonomic workflow • Modular (Drupal) & flexible • Two full time developers • Ecosystem of communities (~450)
  8. 8. Categories of Scratchpads Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
  9. 9. What can Scratchpads do? +Administration +Groups +Specimens -Change your site information -Creating a group -Creating a record -Change you front page -Subscribing to a group -Importing from a spreadsheet -Change your logo +Image -Linking specimen & location records -Activity and access logs -Uploading & basic annotation -Linking specimen & pub. records +Backup -Linking image & location records +Tasks -Backing up your data -Linking image & specimen records -Creating a tasklist -Restoring your data -Linking image & publication records +Taxonomy +Bibliography -Overlay annotations on images -Importing from a spreadsheet -Creating a record +Layout -Importing from ClassificationBank -Importing from a ref. manager -Change your theme -Starting from scratch -Exporting to a reference manager -Menus -Taxonomy manager +Blog -Blocks and sidebars -Displaying a classification -Creating and adding a blog +Locations -Adding names +Custom Content -Creating a record -Deleting names -Defining a CCK -Importing from a spreadsheet -Taxonomy & panels -Importing from a spreadsheet +Pages +Users -Creating a custom view -Creating, editing, cloning & deleting -Your settings +Fileshare -Configuring the panels template -Adding a new user -Creating and using a fileshare +Panels -User roles and permissions +Forum -Adding & configuring content -Adding and editing user profile fields -Altering the forum settings -Creating a new panel -Logging in -Creating a container for a forum -Citing a Panels page +Webform -Creating a new forum +Phylogeny -Creating and using webforms -Creating a new topic inside a forum -Adding a phylogenetic tree
  10. 10. Summary of what Scratchpads can do • Taxon pages, generated from tagged content (plant/animal) • Bibliography management • Character matrixes • Specimen records • Distribution maps (from specimens and regional) • Images, video and sound (bulk import) • Excel spreadsheet import (dynamically generated) • Darwin Core Archive export • Tabular data editing • Custom content • User management • Custom webforms • EOL data import (taxonomy, species information) • GBIF Map integration
  11. 11. Scratchpad v.1 usage (2007- Mar. 2012) Nodes, 430, 948 Sites 326 Users 6809 Active Users 5733 (273 w / 759 m) Users Range: 1-1049 Sites Mean: 15 Mode: 1 • Prof. scientists • Amateur naturalists • Citizen scientists ViBRANT SP 2
  12. 12. Scratchpad 2 – the new version of Scratchpads • Launched March 2012 • 120 sites to date • EOL Fellows • SP1 migration ongoing • More professional • Easier to… - configure (workflows) - navigate (facets) - & populate (MS Excel templates) • Greater standardisation • Still highly flexible • Project profiles (eMonocot) • Framework for integratione.g.
  13. 13. Getting data in and out of Scratchpads 2
  14. 14. Sustainable training, support & development • Wiki - Training manuals, videos & glossary • In-site Support - One click help within your site • Training Courses (12 in 2012) - UK (6), Sweden, (2) Greece (1), Bulgaria (1), South Africa (1), Brazil (1) • Ambassadors Programme - Enthusiastic experienced users - Local support • Embedded Issues Queue - Bug reports - Feature requests • Sandbox Site - • Open Source Development -
  15. 15. Online community revision • Taxonomy is in perpetual beta - Constantly evolving - Changing contributors - Small granular contributions • Sustainability - A permanent space to work - Guaranteed access (2016) - Easy ways to get the data out • Open science - Beyond Open Access - New ways of working - Data management plansFreeloader flies • Need incentives to use - More efficient (functions & reuse) - Attribution & provenance - Credit via citation • New forms of publication
  16. 16. Publishing observations & taxon data > & Specimen records & species Pushed to GBIF & EOL pages on Scratchpads (requires site registration with GBIF & EOL) Darwin Core Archive (DwCA) >19K specimen records >377M specimen records GBIF > 122k species pages > 1 M species pages in EOL
  17. 17. Experiments with article publishing > Paper assembled from XML submission, peer review & Scratchpad database marked-up publication by Pensoft doi:10.3897/zookeys.50.539 XML HTML PDF5-step workflow for selecting data, Published in Zookeys & Phytokeys adding metadata & previewing (worldwide coverage)
  18. 18. Example papers via Scratchpads… Blagoderov V, Hippa H, Nel A (2010). ZooKeys 50: Faulwetter S, Chatzigeorgiou G, Galil BS, Brake I, von Tschirnhaus M (2010). ZooKeys 50: 79–90. doi: 10.3897/zookeys.50.506 Nicolaidou A, Arvanitidis C (2011. ZooKeys 150: 91–96. doi: 10.3897/zookeys.50.505 327–345. doi: 10.3897/zookeys.150.1877 Live (updated) versions of these papers
  19. 19. But… • Limited uptake in 2 years - 1 genus - 6 n. spp - 11 re-descriptions • Software bugs - Pushing the boundaries of SP1 - Fixed in SP2 • Focused on synthetic papers - Not suited to small papers - Less emphasis on data - Hard to properly link in the data • More effort than MS Word - Especially for new SP users
  20. 20. BDJThe Biodiversity Data Journal Making small data big!
  21. 21. Why do we need another new journal!!! Taxonomy needs less fragmentation, not more! BUT… • We need to encourage taxonomists to mobilize & describe their data • This takes considerable effort (e.g. Scratchpads) • “Arguably” this is best rewarded through credit • This means papers and citations • Process must be very easy for authors • Process must facilitate data reuse • Meet “Open Data” policy commitments • The Biodiversity Data Journal is very different…
  22. 22. Biodiversity Data Journal (BDJ)• All data matters: No lower or upper limit of manuscript size!• Multiple publishing routes (not just Scratchpads)• ALL within a single online collaborative platform, including the writing of the manuscript!• New collaborative article authoring tool• Community peer review with “open” &“public” options• This is in addition to conventional peer-review• Online editorial process and version control• Standards-compliant (Darwin Core, Dublin Core, NLM etc.)• Pre-defined Code-compliant article templates
  23. 23. BDJ publication & dissemination workflow GBIF-generated Manuscripts Scratchpads- manuscripts from generated from generated manuscripts metadata descriptions authors’ databases AuthorsConventional manuscripts (MS Word, Open Office) Pensoft Journal System Pensoft Writing Tool (PJS) (PWT) Marked up final publication in PDF, HTML and XML formats
  24. 24. Pensoft manuscript writing tool Contributors • Collaborative online editing (mentor, linguis c editor, copy editor, poten al reviewer, colleague/friend) Con • Rich text capabilities trib u ng • Various templates for taxon treatments Inv ite • Identification keys builder Taxon treatment • Species occurrence data Template- import (Darwin Core based Interac ve key compliant) manuscript Checklist Authoring • Smart citation for figures,Lead author crea on tables, references & Data paper automated positioning Inv ite g • Assembling plates from single figures orin A uth • References import • (CrossRef, PubMed Central, etc.) Co-authors
  25. 25. Testing screenshots of the writing tool Manuscript preview Multi-figure plates Plate layout ID Key ID Key preview builder
  26. 26. Why publish in the BDJ?• Joining (small) data into a large data pool• Open-access, archiving and re-using your data through data aggregators• Providing citation record and creditability for data in the form of peer-reviewed publications• Facilitating online article authoring and editorial process for authors, reviewers and editors• Using a truly innovative dissemination of atomized content• Very low-cost. Free in the launch phase, thereafter at fee that anyone can afford!
  27. 27. 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• ANY KIND of biodiversity-related database, including genomic, ecological and environmental data (data papers)• Biodiversity-related software tools Starting late 2012, early 2013 Recruiting editors now
  28. 28. Acknowledgements • Scratchpad technical development - Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton, Katherine Boulton, • Scratchpad outreach - Irina Brake, Laurence Livermore, Dimitris Koureas • E-Monocot - Paul Wilkin &the Kew team, Charles Godfray & the Oxford team • ViBRANT - Dave Roberts, Lucy Reeve & many many more • Pensoft - Lyubomir Penev, Teodor Georgiev & colleagues • Our 7,000+ users
  29. 29. Penso Penso Peer-review op onsWri ng Journal Public CommunityTool System Closed(PWT) (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
  30. 30. Why we need new methods of publishing… RE-USE of CONTENT Publishing and sharing of primary data Primary data Drawings: Slavena Peneva
  31. 31. Source: Wikipedia