Small pieces loosely joined
A unified theory of biodiversity for the web
Vincent S. Smith

Macro taxonomy
The big picture of taxonomic research
Goal…
• Inventory the Earth’s species
•Document their relationships
• “Publish” these data
Data set…
• 1.8 M described spp. (10M names)
• 300M pages (over last 250 years)
• 1.5-3B specimens
People…
• 4-6,000 scientists
• 30-40,000 “pro-amateurs”
• Many more citizen scientists?

Micro taxonomy
The practice of taxonomic research
Sociology…
• Parochial
• Specialized experts
• Fragmented & distributed
Methodology…
• Different (domain specific)
• Communities of practice
• Non transferable skills
Output…
• Heterogeneous & scattered
• High volume, low impact
• Hard to find (use)
How do we integrate micro &
macro taxonomy for the Web?

Integrating macro & micro taxonomy
Pulling taxonomy and taxonomists together on the Web
The traditional approach…
• Bespoke central database
• Data entry via forms & services
• Output via reports, services & tools
e.g. GBIF, EOL, CBoL, NCBI, CrossRef,
Google Scholar, Species2000 & ITIS
Advantages (Macro-centric) Challenges (Micro-centric)
• Clear fixed input & output • Hard to repurpose (flexibility & agility)
• Top down, multilateral (builds trust) • Build & sustain bottom-up engagement
• Infrastructure robust & sustainable • Resource intensive

http://Scratchpads.eu

What is a Scratchpad?
A website for you & your community
1 2 3
Your data Uploaded & Published & reviewed
tagged on your site

What is a Scratchpad?
A website for you & your community
1 2 3
Your data Uploaded & Published & reviewed
tagged on your site
Fast Intuitive Fit for use

What can Scratchpads do?
Import, manage, search & browse:
Specimens
DNA & Phylogenies
Literature Images

What can Scratchpads do?
Integration & connectivity within & between sites
Specimens
DNA & Phylogenies
Taxonomy
Literature Images

What can Scratchpads do?
In summary:
+Administration +Groups +Specimens
-Change your site information -Creating a group -Creating a record
-Change you front page -Subscribing to a group -Importing from a spreadsheet
-Change your logo +Image -Linking specimen & location records
-Activity and access logs -Uploading & basic annotation -Linking specimen & pub. records
+Backup -Linking image & location records +Tasks
-Backing up your data -Linking image & specimen records -Creating a tasklist
-Restoring your data -Linking image & publication records +Taxonomy
+Bibliography -Overlay annotations on images -Importing from a spreadsheet
-Creating a record +Layout -Importing from ClassificationBank
-Importing from a ref. manager -Change your theme -Starting from scratch
-Exporting to a reference manager -Menus -Taxonomy manager
+Blog -Blocks and sidebars -Displaying a classification
-Creating and adding a blog +Locations -Adding names
+Custom Content -Creating a record -Deleting names
-Defining a CCK -Importing from a spreadsheet -Taxonomy & panels
-Importing from a spreadsheet +Pages +Users
-Creating a custom view -Creating, editing, cloning & deleting -Your settings
+Fileshare -Configuring the panels template -Adding a new user
-Creating and using a fileshare +Panels -User roles and permissions
+Forum -Adding & configuring content -Adding and editing user profile fields
-Altering the forum settings -Creating a new panel -Logging in
-Creating a container for a forum -Citing a Panels page +Webform
-Creating a new forum +Phylogeny -Creating and using webforms
-Creating a new topic inside a forum -Adding a phylogenetic tree

What can Scratchpads do?
Visual taskguide

Current Scratchpads
Ants
Sites: 70+ Bees
Beetles
Users: 850+ Big-headed flies
Birds
Pages: 130k Blackflies
Ciliates
Since March 2007 Cockroaches
Dragon Trees
Dung Beetles
False Buttonweed
Flat worms
Flies
Foraminifera
Fossil Insects
Fungus Gnats
Holometabola
Leaf-miner Flies
Lice
Lichens of Bermuda
Malvaceae
Megalastrum ferns
Milichiid flies
Mosquitoes
Mosses
Nannotax fossils
Nepticuloid moths
Palms
Pearl oysters
Polychaete worms
Scaleworms
Stick insects
Sulawesi Ferns
Termites
Triticid grasses
Weevils
Wood Ferns

Scratchpad visitors
Tracking visitors across sites
Key monthly statistics
- 50,000 page views
- 6,000 visitors
- 8 minutes on site
- 50% returning visits
(average per month 08’)

Scratchpad applications
A multipurpose, flexible technology
eBooks
4th Edition Howard & Moore, Birds of the world
(fact checking, data compilation, 2010, funding)

Scratchpad applications
A multipurpose, flexible technology
eJournals
European Mosquito Bulletin (ISSN 1460-6127), Phasmid Studies (ISSN 0966-0011)
(submission, review, & dissemination of articles)

Scratchpad applications
A multipurpose, flexible technology
Image galleries
Nanno fossils, Cockroaches, Stick insects, Flatworms, Grasses, Lichens & many more…
(rapid upload, annotation, & display of images)

Scratchpad applications
A multipurpose, flexible technology
ZOOTAXA
A rapid international journal for animal taxonomists
ISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition)
Societies & Organizations
GBIF, Zootaxa, Threatened Plants of the World (Kew), BarCoVer (DNA Barcoding) & more
(space for data collection, services, discussion, & organization)

How do Scratchpads work?
Getting a Scratchpad
Requirements
• Biological focus
• Agree to T&C’s (click-thru)
• CC license “by-nc-sa”
Application
http://scratchpads.eu/apply
• Maintainer
• Scope/Mission/API Keys
• (Sub)domain name
Content
• Unrestricted (overlapping)
• No branding (focus on authors)
• Value added

How do Scratchpads work?
Using a Scratchpad
Management
• User categories (maintainer, ed. contrib.)
• Public / private content (flexible groups)
• Admin. page (site settings & behavior)
Data Input
• Content types (biblio, maps, “page” etc)
• Forms, managers, Excel, EndNote etc
• Custom content (add or extend data types)
Tagging (indexing)
• Taxonomy terms (2M +)
• Multiple classifications
• Auto-tagging

Autotagging
Indexing data to make it findable
1. Create content
(e.g. reference)
Journal citation
2. Find terms mentions taxon name
(Autotag)
3. Submit
(Index)

Autotagging
Indexing data to make it findable
1. Create content
(e.g. reference)
2. Find terms
(Autotag)
Matches taxonomy
term (Drag & Drop)
3. Submit
(Index)

Autotagging
Indexing data to make it findable
1. Create content
(e.g. reference)
2. Find terms
(Autotag)
3. Submit Page tagged (indexed)
(Index) with taxon name

How do Scratchpads work?
Indexing data to make it findable
• Tagged data can be
presented differently
• For example as part of
a traditional bibliography
• Or as small windows
or “panels” of data

How do Scratchpads work?
Integrating data & “publishing” in a Scratchpad
Types of Scratchpad Panel…
Built with “tagged data”
Personalized
Common instructions Bibliographic
names literature
Taxonomic Files and
hierarchies documents
Photographs & Specimen
illustrations records
Customized Phylogenetic
content trees

How do Scratchpads work?
Integrating data & “publishing” in a Scratchpad
Dynamically built species pages

How do Scratchpads work?
Integrating data & “publishing” in a Scratchpad
Browsed through a taxonomy

How do Scratchpads work?
Integrating data & “publishing” in a Scratchpad
Including 3rd party content

How do Scratchpads work?
Integrating data & “publishing” in a Scratchpad
With data curation tools

How do Scratchpads work?
Integrating data & “publishing” in a Scratchpad
Listing all “authors”

How do Scratchpads work?
Integrating data & “publishing” in a Scratchpad
Dated, permanent & citable

How do Scratchpads work?
Adjusting the panels layout
Choose which panels to display

How do Scratchpads work?
An example based on the Catalogue of Life classification
2 million taxon pages
Open curation at http://catlife.myspecies.info

Biodiversity on the Web
The informatics landscape

Biodiversity on the Web
Scratchpads are personalizing biodiversity science

Biodiversity on the Web
Scratchpads are pulling and pushing biodiversity data
TapirLink provides TCS over Tapir can
specimens to GBIF provide names and
based on Darwincore classifications

A unified theory of biodiversity?
Scratchpads, EOL and scholarly journals
Encyclopedia Biodiversity
of Life Journals

A unified theory of biodiversity?
Scratchpads, EOL and scholarly journals
?
ZOOTAXA
A rapid international journal for animal taxonomists
ISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition)
15% of all new species descriptions
Approx. 50 new spp. per week!
Encyclopedia Biodiversity
of Life Journals

Scratchpad impact
“Small pieces loosely joined”
1. Bringing data together
Biodiversity studies are data rich, poorly archived & ever changing
2. Bringing people together
Biodiversity researchers are few in number, fragmented & highly distributed
3. Bringing science together
Biodiversity science demands a different approach to addressing BIG questions
BIG IS DIFFERENT!

Thanks…
Simon Rycroft Dave Roberts Kehan Harman
Ben Scott Edward Baker Irina Brake Vladimir Blagoderov

Questions?

Scratchpad management
Scalable & sustainable technology
Hardware, software & user support
Virtual machine, open-source software, self-archiving, backed-up, multi-site configuration
(easy to move & upgrade, secure & reliable, citable, screencasts, low admin., low marginal costs)