Koureas D.N., Van deVelde I., Roberts D.

An Introduction to Scratchpads:

Making your data work for you

keep the discussion going

@vbrant @scratchpads & @dimitriskoureas

at

#piblei

but

what are

the

Scratchpads?

What are Scratchpads?

Hosted websites for biodiversity data

Virtual research & publication platform

Completely open access & open source

Modular & flexible

Facilitate the development of online research communities

Enable users in sharing and interlinking their data

Provide a standardized environment of entering and curating data

Accelerate publication process & dissemination of research products

What are Scratchpads?

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

The Scratchpads concept

Your data External data & services

What Scratchpads are not!

A single biodiversity database

Restricted thematically, geographically or taxonomically

A tool just for taxonomists

Examples of usage:

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

genotypic & morphometric datasets, keys, phylogenies)

ProjectsConservation Regions Societies

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.

How are Scratchpads doing?

In total more than

1,200,000 visitors

How are Scratchpads funded?

2007 2011 2014

ViBRANTVirtual Biodiversity Research

&

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

• 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”

Our informatics grand challenge…

Why Scratchpads?

• 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.

Why Scratchpads?

Vast amounts of unpublished taxonomic “knowledge”

Or

Published knowledge cannot easily be mobilised

Why Scratchpads?

This leads to:

A complex, fragmented & hard to navigate

landscape

Dispersed data sources

Difficulties for collecting information for research

Why Scratchpads?

Science is global

It needs global standards

Global workflows

Cooperation of large institutes and

organisations

Why Scratchpads?

ScratchpadsVirtual Research Environments

Making taxonomy digital, open & linked

the main

features

Classification term oriented system

Biologicalclassifications

Non-biologicalclassifications

Taxonomies Hierarchical controlled vocabularies

The main features

Dynamic Biological Classifications

Manually entered or imported

Auto generated

Nomenclatural annotation

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

Distribution maps

Google maps based

Data layers

Occurrence data

Distribution dataTDWG regions

GBIF data

The main features

Example regional distributionThe main features

Character matrices – Key construction

Quantitative or qualitative characters

Auto generation of keys

Taxon based matrices [Specimens based character matrices]

Media handling

Bulk upload

Metadata (incl. EXIF)

Media galleries

Working groups

Forums

Blog entries

Webforms

Newsletters

RSS syndication

Inbuilt comments

Enhanced communication tools

Generation of custom pages

Tagged or not

External RSS

Twitter feeds

Media files

other

features

Multilanguage support (Localization, Internationalization)

OBOE REST service

other

features

SEO optimization & Google Analytics

Interface customization

Built to interact

Publishing tool

ID Keypreview

Multi-figure plates Plate layout

ID Keybuilder

Manuscript preview

Scratchpads are an integrated system to

Enter, Curate, Mark-up, Link and Publish data

taxonomic workflowin a single virtual environment

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

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

Acknowledgements

and now…

hands-on time

http://pro-ibioXX.taxon.name

http://help.scratchpads.eu/w/Introduction_to_basic_Scratchpad_training_course

your training site:

some dummy data: