ScratchpadsThe 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

What are Scratchpads?

Hosted websites for biodiversity data

Virtual research & publication platform

Completely open access & open source

Modular & flexible

A Scratchpad is a website that holds data for you and your community

The Scratchpads concept

Your data External data & services

Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic

& morphometric datasets, keys, phylogenies)

ProjectsConservation Regions Societies

Examples of use:

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

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/

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

Faceted browsing

An inbuilt Bibliography manager

Taxon tagging and free keywords

Import from and export to all major formats

The main features

Specimen/Observation data

Linked to images and georeferenced

Annotated full specimen/observation records

The main features

Linked to GenBank accession numbers

Distribution maps

Google maps based

Data layers

Occurrence data

Distribution dataTDWG regions

GBIF data

The main features

Example regional distributionThe main features

Create phylogenetic treesBased on Newick/NeXML

Different views

Character matrices – Key construction

Quantitative or qualitative characters

Auto generation of keys

Taxon based matrices [Specimens based character matrices]

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

Working groups

Forums

Blog entries

Webforms

Newsletters

RSS syndication

Inbuilt comments

Enhanced communication tools

The main features

data

mobilisation

more on the way…

External services Integration

IUCN data integration

GBIF distribution data integration

Structured data

Publish, cite,disseminate & archive data

Select, describe &

annotate data

Publication module

Major repositories

Scratchpads Publication Module

Easy & intuitive• Draws on data from your site• Pre-submission validation• Submitted as structured XML• No reformatting

Scratchpads templates for publishing...• Taxon treatments• Nomenclatural acts • Checklists / inventories• Identification keys and trees• Metadata descriptions of databases• Descriptions of software tools

65,000 visitors/month

Per month unique visitors to Scratchpads sites

590 Scratchpads Communities

by 6,800 active registered users

covering 91,631 taxa

in 570,000 pages.

Are Scratchpads sustainable?

In total more than

1,500,000 unique visitors

Are Scratchpads sustainable?

2007 2011 2014

ViBRANTVirtual Biodiversity Research

& &

Other grants in the pipeline

Horizon 2020

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