Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
Scratchpads
The virtual research environment
for biodiversity data

Simon Rycroft, Dave Roberts, Vince Smith, Alice Heaton...
What are Scratchpads?

• Hosted websites for biodiversity data
• Virtual research & publication platform
• Completely open...
The Scratchpads concept
A Scratchpad is a website that holds data for you and your community

Your data

External data & s...
Examples of use:

Taxa
(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic
& morp...
Major integrated project

• 21+ open community sites and
growing
• Over 45 internationally
collaborating scientists

• Sit...
Major integrated project

• Retrieve information on
any Monocot plant
• Rich downloadable data

• Identification keys
• Mo...
The main features
Dynamic Biological Classifications

Manually entered or imported

Auto generated
The main features
Taxon pages
Overview of data related to taxon

Generated from tagged content
The main features
Bibliography management

An inbuilt Bibliography manager

Faceted browsing
Taxon tagging and free keywor...
The main features
Specimen/Observation data

Annotated full specimen/observation records
Linked to images and georeference...
The main features
Distribution maps
Google maps based

Data layers
Occurrence data

Distribution data
TDWG regions

GBIF d...
The main features

Example regional distribution
Create phylogenetic trees
Based on Newick/NeXML
Different views
The main features
Character matrices – Key construction

Quantitative or qualitative characters
Auto generation of keys
Ta...
The main features
Media handling

Bulk upload
Metadata
(EXIF & Audubon core)

Media galleries
The main features
Generation of custom pages

Tagged or not
External RSS
Twitter feeds
Media files
The main features
Enhanced communication tools

Working groups

Forums
Blog entries
Webforms
Newsletters
RSS syndication
I...
External services Integration
data

mobilisation

more on the way…
IUCN data integration
GBIF distribution data integration
Structured data

Select,
describe &
annotate data

Publication module

Publish, cite,
disseminate &
archive data

Major re...
Scratchpads Publication Module
Scratchpads templates for publishing...
• Taxon treatments
• Nomenclatural acts
• Checklist...
Are Scratchpads sustainable?

590 Scratchpads Communities
by

6,800 active registered users

covering

91,631 taxa

in 570...
Are Scratchpads sustainable?

2007

2011

2014

ViBRANT
Virtual Biodiversity Research

&

&

Other grants in the pipeline
...
About
scratchpads.eu
Code
git.scratchpads.eu
Try
sandbox.scratchpads.eu
Scratchpads: the Virtual Research Environment for biodiversity data
Scratchpads: the Virtual Research Environment for biodiversity data
Upcoming SlideShare
Loading in …5
×

Scratchpads: the Virtual Research Environment for biodiversity data

968 views

Published on

Rycroft, S., Roberts, D., Smith, V., Heaton, A., Bouton, K., Livermore, L., Koureas, D., Baker, E. 2013. Scratchpads: the Virtual Research Environment for biodiversity data. TDWG, Biodiversity Information Standards. Grand Hotel Mediterraneo Florence, Italy, 27 Oct - 1 Nov., 2013.

Published in: Technology
  • Be the first to comment

  • Be the first to like this

Scratchpads: the Virtual Research Environment for biodiversity data

  1. 1. Scratchpads The virtual research environment for biodiversity data Simon Rycroft, Dave Roberts, Vince Smith, Alice Heaton, Katherine Bouton, Laurence Livermore, Dimitris Koureas, Ed Baker Natural History Museum, London
  2. 2. What are Scratchpads? • Hosted websites for biodiversity data • Virtual research & publication platform • Completely open access & open source • Modular & flexible
  3. 3. The Scratchpads concept A Scratchpad is a website that holds data for you and your community Your data External data & services
  4. 4. Examples of use: Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
  5. 5. Major integrated project • 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
  6. 6. Major integrated project • Retrieve information on any Monocot plant • Rich downloadable data • Identification keys • Model example of linked attributed data eMonocot Portal: http://e-monocot.org/
  7. 7. The main features Dynamic Biological Classifications Manually entered or imported Auto generated
  8. 8. The main features Taxon pages Overview of data related to taxon Generated from tagged content
  9. 9. The main features Bibliography management An inbuilt Bibliography manager Faceted browsing Taxon tagging and free keywords Import from and export to all major formats
  10. 10. The main features Specimen/Observation data Annotated full specimen/observation records Linked to images and georeferenced Linked to GenBank accession numbers
  11. 11. The main features Distribution maps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data
  12. 12. The main features Example regional distribution
  13. 13. Create phylogenetic trees Based on Newick/NeXML Different views
  14. 14. The main features Character matrices – Key construction Quantitative or qualitative characters Auto generation of keys Taxon based matrices [Specimens based character matrices]
  15. 15. The main features Media handling Bulk upload Metadata (EXIF & Audubon core) Media galleries
  16. 16. The main features Generation of custom pages Tagged or not External RSS Twitter feeds Media files
  17. 17. The main features Enhanced communication tools Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments
  18. 18. External services Integration data mobilisation more on the way…
  19. 19. IUCN data integration
  20. 20. GBIF distribution data integration
  21. 21. Structured data Select, describe & annotate data Publication module Publish, cite, disseminate & archive data Major repositories
  22. 22. Scratchpads Publication Module Scratchpads templates for publishing... • Taxon treatments • Nomenclatural acts • Checklists / inventories • Identification keys and trees • Metadata descriptions of databases • Descriptions of software tools Easy & intuitive • Draws on data from your site • Pre-submission validation • Submitted as structured XML • No reformatting
  23. 23. Are Scratchpads sustainable? 590 Scratchpads Communities by 6,800 active registered users covering 91,631 taxa in 570,000 pages. In total more than 1,500,000 unique visitors Per month unique visitors to Scratchpads sites 65,000 visitors/month
  24. 24. Are Scratchpads sustainable? 2007 2011 2014 ViBRANT Virtual Biodiversity Research & & Other grants in the pipeline Horizon 2020
  25. 25. About scratchpads.eu Code git.scratchpads.eu Try sandbox.scratchpads.eu

×