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

2. 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 Our current taxonomic data production 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 undescribed 1 1 How Many Species Are There on Earth and in the Ocean? Mora C et al. doi:10.1371/journal.pbio.1001127

4. Expected volume of taxonomic and biodiversity data Need of extracting, aggregating and linking data on a global level

5. The four nodes of data workflow 1. We collect and generate data 2. We curate, link and structure data 3. We analyse data 4. We publish data

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

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

8. Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001 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” To achieve this…

9. Scratchpads Virtual Research Environments Making taxonomy digital, open & linked

10. so… what are 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? development of online research communities facilitate standardized environment of entering and curating data through sharing and interlinking that allow dissemination of research products and

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

14. The Scratchpads concept

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

16. Red List conservation assessments Examples of use:

17. Bulbous monocot genera listed in CITES

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

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. 65000 unique visitors/month Per month unique visitors to Scratchpads sites 464 Scratchpads Communities by 6,407 active registered users covering 52,661 taxa in 559,488 pages. Are Scratchpads sustainable? In total more than 1,200,000 visitors

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

24. the main features

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

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

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

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

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

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

31. Example regional distribution The main features

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

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

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

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

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

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

39. IUCN data integration

40. GBIF data integration

41. BRAHMS data migration

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

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. Allow submission of datasets for publication without reformatting and restructuring Working in a single environment based on standardised XML schema

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

47. The data workflow MANUSCRIPT PUBLISHED (XML, PDF) MANUSCRIPT PUBLISHED (XML, PDF) PENSOFT JOURNAL SYSTEM (PJS 2.0) XML submission SCRATCHPADS Community Taxon namesOccurrence datadatasets Archive Taxon treatments Plazi Wiki

48. Scratchpads are an integrated system to Enter, Curate, Mark-up, Link and Publish data taxonomic workflow in a single virtual environment

49. 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 - Lyobomir Penev and the Pensoft team Our 7000 users Acknowledgements

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

51. Thank you Data curation Data curation Data analysis Data analysis Data publishing Data publishing Data collection & generation Data collection & generation

53. Authors and Contributors Manuscript ready to submit

54. However… not publicly accessible lack sufficient contextual metadata published in formats that require time-consuming manual extraction difficulty in publishing valuable datasets (i.a. local or regional Floras, Faunas) Published knowledge cannot easily be mobilised Vast amounts of unpublished taxonomic “knowledge”