1) Scratchpads are digital workspaces for collaboratively building biodiversity data and publishing information. Over 239 sites and 3,000+ users have used Scratchpads since 2007. 2) An updated version, Scratchpads 2, is scheduled for release in January 2012. It will include new technical features and user enhancements to better support collaboration and scholarly publication. 3) Long term, Scratchpads aim to serve as a fully digital scholarly communication system integrated throughout the entire research process, from assembling data to formal publication. Current publishing efforts via Scratchpads include open access journals and data publishing.

1. Scratchpads
Past, present & future
Ed Baker
Natural History Museum, London
edwab@nhm.ac.uk

2. Scratchpads: the concept
1 2 3
Your data Uploaded & “Published” & reviewed
tagged on your site
Fast Intuitive Fit for use
http://scratchpads.eu

3. Scratchpads: 2007-2011
http://scratchpads.eu/siteslist

4. Scratchpad usecases
http://scratchpads.eu/siteslist

5. Scratchpad usecases
http://scratchpads.eu/siteslist

6. Scratchpad usage
Mar. 2007 - Dec. 2010
25 May, 2011
239 sites
3212 users
371,947 nodes

7. Scratchpads: the present
Financial support until Dec. 2013
ViBRANT
Virtual Biodiversity

8. Scratchpads 2
• Scheduled for January 2012 (5 years after Scratchpad 1)
• Move from Drupal 6 to Drupal 7 (4 year upgrade cycle, UI + entities)
• 67 Contributed modules (31 done, 14 untested, 22 to do)
• 52 Scratchpad modules (28 done, 14 untested, 10 to do)
• Migrate current Scratchpads
• New technical enhancements (hosting env., git, services, registry…)
- supporting sustainability
• New user features (theme, workflow, spp. pages, mapping, services)
- supporting “publication”
http://wiki.scratchpads.eu/w/Wp2

9. Scratchpads 2: user enhancements
Consistent Scratchpad theme
• Most sites use Garland (improves site looks)
• Idiosyncratic (colours & layouts)
• Sp2 more professional & scholarly
• Some flexibility (site profiles)

10. Scratchpads 2: user enhancements
Improved administrative interface & workflows
• Basic vs. advanced admin
• Poor findability, hard to use
• Hide unnecessary items
• Workflow complex functions 2
1
- Integrate complex actions
- Guide the user through each step 3
o Adding users
o Site setup functions
o Groups & permissions
o Edit / add content types
4
o Importing content & taxonomy
o Creating services 5
o Creating views
o “Pages” menu concept

11. Scratchpads 2: user enhancements
Project themed scratchpads
• New site management system (Aegir)
• Support project specific profiles
• themes, modules & wokflows
• Example themes include
• eMonocot sites
• GBIF Nodes Portal Toolkit
• EOL LifeDesks?

12. Scratchpads 2: user enhancements
New species pages
• Directly edit the page
• Better presentation
• Tabs (myspecies / ispecies)
• Data inheritance (parent-child)
• Better content controls
• More intelligent ispecies filters

13. Scratchpads 2: user enhancements
Integrated mapping
• 3 current map types
GBIF occurrence records
Areas (TDWG level 4)
Specimen point localities

14. Scratchpads 2: user enhancements
Integrated mapping
• 3 current map types Edit point
metadata on map
• All integrated & editable in Scratchpads 2
TDWG area data
(from Scratchpads)
Point localities
(from Scratchpads)
Point localities
(from GBIF)
Point localities
(from flickr)
Areas (TDWG level 4)

15. Scratchpads: the future
A natively digital scholarly communication system
• The article was (is) the unit of scholarly comm. (350yrs)
• Research practices have moved on
o Highly collaborative, data intensive & networked
• Scholarly communication has not adapted (e.g. the PDF)
• Published “knowledge” hides “dark data”
• Need a natively digital scholarly communication system
o Must support end-to-end the lifecycle of data, information & knowledge
“the future scholarly communication system should
closely resemble—and be intertwined with—the
scholarly endeavor itself, rather than being
its after-thought or annex” Sompel et al 2004. http://bit.ly/
Van de
a3o9UX

16. Current publishing efforts on Scratchpads
1. Low cost journal infrastructure
• Scratchpads used to publish PDFs (1,000’s)
• Independent editorial control & peer review
• Free to publish, open access, no page limits
• ISBN’s, but no doi’s, PubMed or ISI impact
• No online submission, just static PDFs

17. Current publishing efforts on Scratchpads
2. Simple data publishing > GBIF
Specimen records Pushed to 3rd party specialist
on Scratchpads data publishers
>18K specimen records >276M specimen records
(local small scale coverage) (worldwide coverage)

18. Next generation article publishing
3. From prototype to operation
Paper assembled from XML submission, peer review &
Scratchpad database marked-up publication by Pensoft
doi:10.3897/zookeys.50.539
5-step workflow for selecting data, XML
HTML
PDF
Published in Zookeys & Phytokeys
adding metadata & previewing (worldwide coverage)

19. Next generation data publishing
4. Formally publishing metadata descriptions of datasets
Dataset & metadata description Dataset description reviewed,
assembled in Scratchpad published & citable from new journal
Dataset
doi:xxxx.50.539 doi:10.3897/biodat.50.539
Datasets built & described via a Dataset description published in
Scratchpad & dataset deposited in new data publication journal
permanent repository