Scratchpads

1. Scratchpads Virtual Research Environments for taxonomic and biodiversity related data Reading, 27-02-2013

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 projects Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.

3. On the other hand: Estimates of 7.5 million species still undescribed1 1How Many Species Are There on Earth and in the Ocean? Mora C et al. doi:10.1371/journal.pbio.1001127

4. Expected volume of taxonomicandbiodiversity data Need of extracting, aggregatingandlinkingdataon a global level

5. The four nodes of data workflow 1. We collect and generatedata 2.We curate, link and structure data 3.We analysedata 4.We publishdata

6. The four nodes of data workflow What are the bottlenecks in the workflow? Data collection & generation Data publishing Data curation Data analysis

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

8. To achieve this… • This requires data, information & knowledge to be… • Digital • Not printed paper • Openly accessible • Not behind barriers (e.g. paywalls) • Linked-up • Not in silos “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

9. ScratchpadsVirtual Research Environments Making taxonomy digital, open & linked

10. so… whatare the Scratchpads?

11. What are Scratchpads? Hosted websites for biodiversity data Virtual research & publication platform Completely open access & open source Modular & flexible

12. What are Scratchpads? facilitate development of online research communities through standardized environment of entering and curating data that allow sharing and interlinking and dissemination of research products

13. A Scratchpad is a website that holds data for you and your community The Scratchpads concept External data & services Your data

14. The Scratchpads concept

15. Examples of use: Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies

16. Examples of use: Red List conservation assessments

17. Examples of use: Bulbous monocot genera listed in CITES

18. Examples of use: Global Invasive Alien Species Information Partnership

19. Major integrated projects • Online resource for monocot plants • Collaboration between Kew, Oxford University and NHM • Data to be open and usable by other scientists

20. Major integrated projects • 21+ open community sites and growing • Over 45 internationally collaborating scientists • Site data feeds into a “Portal” Site List: http://about.e-monocot.org/list-emonocot-scratchpads

21. Major integrated projects • Retrieve information on any Monocot plant • Rich downloadable data • Identification keys • Model example of linked attributed data eMonocot Portal: http://e-monocot.org/

22. Are Scratchpads sustainable? 464 Scratchpads Communities by 6,407 active registered users covering 52,661 taxa in 559,488 pages. In total more than1,200,000 visitors Per month unique visitors to Scratchpads sites 65000 unique visitors/month

23. Are Scratchpads sustainable? 2011 2007 2014 ViBRANT Virtual Biodiversity Research & & Other grants in the pipeline Proposals?

24. the main features

25. The main features Classification term oriented system Biological classifications Non-biological classifications Taxonomies Hierarchical controlled vocabularies

26. The main features Dynamic Biological Classifications Manually entered or imported Auto generated

27. The main features Taxon pages Overview of data related to taxon Generated from tagged content

28. The main features Bibliography management An inbuilt Bibliography manager Faceted browsing Taxon tagging and free keywords Import from and export to all major formats

29. The main features Specimen/Observation data Annotated full specimen/observation records Linked to images and georeferenced

30. The main features Distribution maps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data

31. Example regional distribution The main features

32. The main features Character matrices – Key construction Quantitative or qualitative characters Auto generation of keys Taxon based matrices [Specimens based character matrices]

33. The main features Media handling Bulk upload Metadata (incl. EXIF) Media galleries

34. The main features Generation of custom pages Tagged or not External RSS Twitter feeds Media files

35. The main features Enhanced communication tools Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments

36. The main features analytical tools OBOE service i.a. Ecological informatics, Phylogenetics, Sequence alignment

38. External services Integration data mobilisation more on the way…

39. IUCN data integration

40. GBIF data integration

41. BRAHMS data migration

42. The main features The Publication module Open-access journal

43. 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

44. How do Scratchpads and BDJ interact?

45. Working in a single environment Allowsubmission of datasets for publication without reformattingand restructuring based on standardised XML schema

46. The publication module Author names and affiliations Taxon descriptions Specimen data Figures and Tables XML Keys References Texts

47. The data workflow XML submission PENSOFT JOURNAL SYSTEM (PJS 2.0) Scratchpads Community MANUSCRIPT published (XML, PDF) Archive datasets Occurrence data Taxon treatments Taxon names Wiki Plazi

48. Scratchpads are an integrated system to Enter, Curate, Mark-up, Link and Publish data taxonomicworkflow in asinglevirtualenvironment

49. Acknowledgements • Scratchpads technical development • Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Bouton • Scratchpads outreach • Laurence Livermore, Isa van deVelde & Dimitris Koureas • e-Monocot • Paul Wilkin & the Kew team, Charles Godfray & the Oxford team • ViBRANT • Vince Smith, Dave Roberts & Lucy Reeve • Pensoft • - LyobomirPenev and the Pensoft team • Our 7000 users

50. Help & Support • In-site Support • Wiki • Training Courses (12 in 2012) • Ambassadors Programme • Embedded Issues Queue • Sandbox Site http://help.scratchpad.eu