Small pieces loosely joined: a unified theory of biodiversity for the web.
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Vincent S. Smith
Small pieces loosely joinedA unified theory of biodiversity for the web
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Macro taxonomyThe big picture of taxonomic research
• Inventory the Earth’s species•Document their relationships• “Publish” these data
Goal…
• 1.8 M described spp. (10M names)• 300M pages (over last 250 years)• 1.5-3B specimens
Data set…
People…• 4-6,000 scientists• 30-40,000 “pro-amateurs”• Many more citizen scientists?
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Micro taxonomyThe practice of taxonomic research
How do we integrate micro ¯o taxonomy for the Web?
• Parochial• Specialized experts• Fragmented & distributed
Sociology…
• Different (domain specific)• Communities of practice• Non transferable skills
Methodology…
Output…• Heterogeneous & scattered• High volume, low impact• Hard to find (use)
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Integrating macro & micro taxonomyPulling taxonomy and taxonomists together on the Web
e.g. GBIF, EOL, CBoL, NCBI, CrossRef,Google Scholar, Species2000 & ITIS
• Bespoke central database• Data entry via forms & services• Output via reports, services & tools
The traditional approach…
• Clear fixed input & output• Top down, multilateral (builds trust)• Infrastructure robust & sustainable
Advantages• Hard to repurpose (flexibility & agility)• Build & sustain bottom-up engagement• Resource intensive
Challenges(Macro-centric) (Micro-centric)
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http://Scratchpads.eu
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What is a Scratchpad?A website for you & your community
Your data1
Published & reviewedon your site
3Uploaded &
tagged
2
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Your data1
Published & reviewedon your site
3Uploaded &
tagged
2
Fast Intuitive Fit for use
What is a Scratchpad?A website for you & your community
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What can Scratchpads do?Import, manage, search & browse:
DNA & Phylogenies
Specimens
Literature Images
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DNA & Phylogenies
Specimens
Literature ImagesTaxonomy
What can Scratchpads do?Integration & connectivity within & between sites
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+Administration -Change your site information -Change you front page -Change your logo -Activity and access logs+Backup -Backing up your data -Restoring your data+Bibliography -Creating a record -Importing from a ref. manager -Exporting to a reference manager+Blog -Creating and adding a blog+Custom Content -Defining a CCK -Importing from a spreadsheet -Creating a custom view+Fileshare -Creating and using a fileshare+Forum -Altering the forum settings -Creating a container for a forum -Creating a new forum -Creating a new topic inside a forum
+Groups -Creating a group -Subscribing to a group+Image -Uploading & basic annotation -Linking image & location records -Linking image & specimen records -Linking image & publication records -Overlay annotations on images+Layout -Change your theme -Menus -Blocks and sidebars+Locations -Creating a record -Importing from a spreadsheet+Pages -Creating, editing, cloning & deleting -Configuring the panels template+Panels -Adding & configuring content -Creating a new panel -Citing a Panels page+Phylogeny -Adding a phylogenetic tree
+Specimens -Creating a record -Importing from a spreadsheet -Linking specimen & location records -Linking specimen & pub. records+Tasks -Creating a tasklist+Taxonomy -Importing from a spreadsheet -Importing from ClassificationBank -Starting from scratch -Taxonomy manager -Displaying a classification -Adding names -Deleting names -Taxonomy & panels+Users -Your settings -Adding a new user -User roles and permissions -Adding and editing user profile fields -Logging in+Webform -Creating and using webforms
What can Scratchpads do?In summary:
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What can Scratchpads do?Visual taskguide
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Current ScratchpadsAntsBeesBeetlesBig-headed fliesBirdsBlackfliesCiliatesCockroachesDragon TreesDung BeetlesFalse ButtonweedFlat wormsFliesForaminiferaFossil InsectsFungus GnatsHolometabolaLeaf-miner FliesLiceLichens of BermudaMalvaceaeMegalastrum fernsMilichiid fliesMosquitoesMossesNannotax fossilsNepticuloid mothsPalmsPearl oystersPolychaete wormsScaleworms
TermitesTriticid grassesWeevilsWood Ferns
Sulawesi FernsStick insects
Sites: 70+Users: 850+Pages: 130kSince March 2007
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Scratchpad visitorsTracking visitors across sites
Key monthly statistics- 50,000 page views - 6,000 visitors- 8 minutes on site- 50% returning visits
(average per month 08’)
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Scratchpad applicationsA multipurpose, flexible technology
4th Edition Howard & Moore, Birds of the world(fact checking, data compilation, 2010, funding)
eBooks
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European Mosquito Bulletin (ISSN 1460-6127), Phasmid Studies (ISSN 0966-0011)(submission, review, & dissemination of articles)
eJournals
Scratchpad applicationsA multipurpose, flexible technology
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Image galleriesNanno fossils, Cockroaches, Stick insects, Flatworms, Grasses, Lichens & many more…
(rapid upload, annotation, & display of images)
Scratchpad applicationsA multipurpose, flexible technology
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ZOOTAXAA rapid international journal for animal taxonomistsISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition)
GBIF, Zootaxa, Threatened Plants of the World (Kew), BarCoVer (DNA Barcoding) & more (space for data collection, services, discussion, & organization)
Societies & Organizations
Scratchpad applicationsA multipurpose, flexible technology
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How do Scratchpads work?Getting a Scratchpad
• Biological focus• Agree to T&C’s (click-thru)• CC license “by-nc-sa”
Requirements
• Maintainer• Scope/Mission/API Keys• (Sub)domain name
Application
Content• Unrestricted (overlapping)• No branding (focus on authors)• Value added
http://scratchpads.eu/apply
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Using a Scratchpad
• User categories (maintainer, ed. contrib.)• Public / private content (flexible groups)• Admin. page (site settings & behavior)
Management
• Content types (biblio, maps, “page” etc)• Forms, managers, Excel, EndNote etc• Custom content (add or extend data types)
Data Input
Tagging (indexing)• Taxonomy terms (2M +)• Multiple classifications• Auto-tagging
How do Scratchpads work?
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AutotaggingIndexing data to make it findable
1. Create content
2. Find terms
3. Submit(Index)
(Autotag)
(e.g. reference)
Journal citationmentions taxon name
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1. Create content
2. Find terms
3. Submit(Index)
(Autotag)
(e.g. reference)
Matches taxonomyterm (Drag & Drop)
AutotaggingIndexing data to make it findable
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1. Create content
2. Find terms
3. Submit(Index)
(Autotag)
(e.g. reference)
Page tagged (indexed)with taxon name
AutotaggingIndexing data to make it findable
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Indexing data to make it findable
How do Scratchpads work?
• Tagged data can bepresented differently
• For example as part ofa traditional bibliography
• Or as small windowsor “panels” of data
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Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
Taxonomichierarchies
Files anddocuments
Phylogenetictrees
Customizedcontent
Specimenrecords
Photographs &illustrations
PersonalizedinstructionsCommon
namesBibliographic
literature
Types of Scratchpad Panel…Built with “tagged data”
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Dynamically built species pages
Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
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Browsed through a taxonomy
Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
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Including 3rd party content
Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
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With data curation toolsWith data curation tools
Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
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Listing all “authors”
Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
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Dated, permanent & citable
Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
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Choose which panels to display
Adjusting the panels layout
How do Scratchpads work?
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An example based on the Catalogue of Life classification
How do Scratchpads work?
2 million taxon pagesOpen curation at http://catlife.myspecies.info
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The informatics landscape
Biodiversity on the Web
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Scratchpads are personalizing biodiversity science
Biodiversity on the Web
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Scratchpads are pulling and pushing biodiversity data
Biodiversity on the Web
TapirLink providesspecimens to GBIF
based on Darwincore
TCS over Tapir canprovide names and
classifications
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BiodiversityJournals
Encyclopediaof Life
Scratchpads, EOL and scholarly journals
A unified theory of biodiversity?
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Scratchpads, EOL and scholarly journals
A unified theory of biodiversity?
?
Encyclopediaof Life
ZOOTAXAA rapid international journal for animal taxonomistsISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition)
15% of all new species descriptionsApprox. 50 new spp. per week!
BiodiversityJournals
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“Small pieces loosely joined”
Scratchpad impact
1. Bringing data togetherBiodiversity studies are data rich, poorly archived & ever changing
2. Bringing people togetherBiodiversity researchers are few in number, fragmented & highly distributed
3. Bringing science togetherBiodiversity science demands a different approach to addressing BIG questions
BIG IS DIFFERENT!
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Ben Scott Vladimir BlagoderovIrina BrakeEdward Baker
Thanks…
Simon Rycroft Dave Roberts Kehan Harman
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Questions?
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Scalable & sustainable technology
Scratchpad management
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)
Hardware, software & user support