This is the introduction presentation for the basic Scratchpads training course

1. An Introduction to
Scratchpads:
Making your data work for you
Koureas D.N., Van deVelde I., Roberts D.

2. keep the discussion going
@vbrant @scratchpads &
@dimitriskoureas
at
#piblei

3. but
what are
the
Scratchpads?

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

5. What are Scratchpads?
Facilitate the development of online research communities
Provide a standardized environment of entering and curating data
Enable users in sharing and interlinking their data
Accelerate publication process & dissemination of research products

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

7. What Scratchpads are not!
A single biodiversity database
Restricted thematically, geographically or taxonomically
A tool just for taxonomists

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

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

10. How are Scratchpads funded?
2007 2011 2014
ViBRANT
Virtual Biodiversity Research
&

11. Why Scratchpads?
Our informatics grand challenge…
“Link together evolutionary This requires data, information & knowledge
data… by developing analytical to be…
tools and proper • Digital
documentation and then use Not printed paper
this framework to conduct • Openly accessible
comparative analyses, studies Not behind barriers
of evolutionary process and • Linked-up
biodiversity analyses” Not in silos
Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page.
TREE. doi:10.1016/j.tree.2011.11.001

12. Why Scratchpads?
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.

13. Why Scratchpads?
Vast amounts of unpublished taxonomic “knowledge”
Or
Published knowledge cannot easily be mobilised

14. Why Scratchpads?
This leads to:
• A complex, fragmented & hard to navigate landscape
• Dispersed data sources
• Difficulties for collecting information for research

15. Why Scratchpads?
• Science is global
• It needs global standards
• Global workflows
• Cooperation of large institutes and
organisations

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

17. the main
features

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

19. The main features
Dynamic Biological Classifications
Manually entered or imported
Auto generated
Nomenclatural annotation

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

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

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

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

24. The main features
Example regional distribution

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

26. Media handling
Bulk upload
Metadata (incl. EXIF)
Media galleries

27. Enhanced communication tools
Working groups
Forums
Blog entries
Webforms
Newsletters
RSS syndication
Inbuilt comments

28. Generation of custom pages
Tagged or not
External RSS
Twitter feeds
Media files

29. other
features
Multilanguage support (Localization, Internationalization)
OBOE REST service

30. other
features
SEO optimization & Google Analytics
Interface customization

31. Built to interact

32. Publishing tool
Manuscript preview Multi-figure plates Plate layout
ID Key ID Key
preview builder

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

34. Help & Support
• In-site Support
- One click help within your site
• Wiki
- Training manuals, videos & glossary
• 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
- http://sandbox.scratchpad.eu
http://help.scratchpad.eu

35. Acknowledgements
Scratchpad technical development
- Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Bouton
Scratchpad outreach
- Isa van deVelde, Laurence Livermore & Dimitris Koureas
E-Monocot
- Paul Wilkin & the Kew team, Charles Godfray & the Oxford team
ViBRANT
- Vince Smith, Dave Roberts & Lucy Reeve
Our 7,000+ users

36. and now…
hands-on time
your training site:
http://pro-ibioXX.taxon.name
some dummy data:
http://help.scratchpads.eu/w/
Introduction_to_basic_Scratchpad_training_course