Small pieces loosely joined: towards a unified theory of biodiversity for the web
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Transcript of Small pieces loosely joined: towards a unified theory of biodiversity for the web
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?
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)
What is a Scratchpad?A website for you & your community
Your data1
Published & reviewedon your site
3Uploaded &
tagged
2
Your data1
Published & reviewedon your site
3Uploaded &
tagged
2
Fast Intuitive Fit for use
What is a Scratchpad?A website for you & your community
What can Scratchpads do?Import, manage, search & browse:
DNA & Phylogenies
Specimens
Literature Images
DNA & Phylogenies
Specimens
Literature ImagesTaxonomy
What can Scratchpads do?Integration & connectivity within & between sites
+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:
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
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 visitors
Scratchpad applicationsA multipurpose, flexible technology
4th Edition Howard & Moore, Birds of the world(fact checking, data compilation, 2010, funding)
eBooks
European Mosquito Bulletin (ISSN 1460-6127), Phasmid Studies (ISSN 0966-0011)(submission, review, & dissemination of articles)
eJournals
Scratchpad applicationsA multipurpose, flexible technology
Image galleriesNanno fossils, Cockroaches, Stick insects, Flatworms, Grasses, Lichens & many more…
(rapid upload, annotation, & display of images)
Scratchpad applicationsA multipurpose, flexible technology
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
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?
AutotaggingIndexing data to make it findable
1. Create content
2. Find terms
3. Submit(Index)
(Autotag)
(e.g. reference)
Journal citationmentions taxon name
1. Create content
2. Find terms
3. Submit(Index)
(Autotag)
(e.g. reference)
Matches taxonomyterm (Drag & Drop)
AutotaggingIndexing data to make it findable
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
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
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”
Dynamically built species pages
Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
Including 3rd party content
Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
With data curation toolsWith data curation tools
Integrating data & “publishing” in a Scratchpad
How do Scratchpads work?
An example based on the Catalogue of Life classification
How do Scratchpads work?
2 million taxon pagesOpen curation at http://catlife.myspecies.info
Biodiversity Heritage Library• Digitising heritage literature
Encyclopedia of Life• A web page for every species
Scholarly Journals• Traditional publishing
BHL, EOL and scholarly journals
A unified theory of biodiversity?
• Biodiversity publications since 1469- 5.4 million books- 800,000 monographs- 40,000 periodicals
• Held by Natural History librariesE.g., NHM holds more than 1M books, 250kmonographs & periodicals, 0.5M artworks
• Sharing the digisation of contents• Focus on out of copyright materials• Partnership with “Internet Archive”
• BHL partnership of 10 Nat. Hist. libraries
• Make the contents “findable”
“Digitizing biodiversity literature”
Biodiversity Heritage Library
1 scribe machine, 3,500 pages per shift per day
2. Extract text (OCR)
1. Scan (photograph)
34 scribe machines now in operation
3. Find keywords- Taxonomic names- Author names- Citations- Collection data- Morphological data- Descriptions- Identification keys- Illustrations- Photographs
“Digitizing biodiversity literature”
Biodiversity Heritage Library
2. Extract text (OCR)
3. Find keywords
1. Scan
- Taxonomic names- Author names- Citations- Collection data- Morphological data- Descriptions- Identification keys- Illustrations- Photographs
Palma, R.L., andR.L.C. Pilgrim.2002. A revisionof the genusNaubates(Insecta:Phthiraptera:Philopteridae).J. R. Soc. N.Z.32:7-60.
“Digitizing biodiversity literature”
Biodiversity Heritage Library
2. Extract text (OCR)
3. Find keywords
1. Scan
- Taxonomic names- Author names- Citations- Collection data- Morphological data- Descriptions- Identification keys- Illustrations- Photographs
4. Index
5. Put on the web
Palma, R.L., andR.L.C. Pilgrim.2002. A revisionof the genusNaubates(Insecta:Phthiraptera:Philopteridae).J. R. Soc. N.Z.32:7-60.6. 10M pp. to date
“Digitizing biodiversity literature”
Biodiversity Heritage Library
Scratchpads as a tool to add articles (and markup) to BHL?
Creating a community built virtual taxonomic library
Scratchpads and BHL
NotYet?Yes
• A web page for all 1.8M species
• $25m funding (5 years)- MacArthur and Sloan Foundations
• Megascience mashup- Aggregating data from the web
• Multiple audiences- Science & outreach
• 10 years to complete- First draft 2008, “finished” 2017!
“A web page for every species”
Encyclopedia of Life
• Struggling to find an identity?- Competition, vetting, growth, credit
• A possible publishing platform?- LifeDesks / Scratchpads
BiodiversityJournals
• Fragmented
• Mostly commercial
• Data poor• Fixed audience
- Hard to repurpose
• Possible role for EoL?- Web publishing platform (cf Wikipedia)
• Zootaxa- 15% n. spp; 50 spp. a week!
Scholarly communication in taxonomy & systematics
Journals Articles
• Scratchpads / EoL / Zootaxa- MS Word Template (markup)- Simultaneous publication
“Small pieces loosely joined”
Summary
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 DIFFERENTNew opportunities & new challenges!
Ben Scott Vladimir BlagoderovIrina BrakeEdward Baker
Thanks…
Simon Rycroft Dave Roberts Kehan Harman