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Smith, VS.* (2008)Cybertaxonomy: applying computers & the Web the study of biodiversity.
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Vincent S. Smith
CybertaxonomyApplying computers & the Webto the study of biodiversity
Proportion of all 1.8 milliondescribed species
Insects
ArachnidsCrustaceans 2.4%
Other Arthropods 1.2%Molluscs
Nematodes 0.9%Other Invertebrates
Vertebrates
Plants
FungiAlgae
Protozoans
56.3%
4.5%
4.2%
4.0%2.7%
14.3%
4.2%2.4%2.4%
Bacteria andViruses 0.5%
Biodiversity ScienceThe foundation of all biology
Goals…• Inventory the Earth’s species• Understand their relationships• “Publish” these data
Data…• 1.8M described species (10M names)
• 300M pages (over last 250 years)
• 1.5-3B specimens• Up to 87% of life undescribed!
People…• 4-6,000 scientists• 30-40,000 amateurs• Many more citizen scientists?• 6% scientists cover 80% of biodiversity
Cybertaxonomy
Encyclopedia of Life• A web page for every species
Biodiversity Heritage Library• Digitising biodiversity literature
BiodiversityHeritageLibrary
Scratchpads• Your biodiversity data on the Web
Applying computers & the web to the study of biodiversity
Cybertaxonomy
Encyclopedia of Life• A web page for every species
Biodiversity Heritage Library• Digitising biodiversity literature
BiodiversityHeritageLibrary
Scratchpads• Your biodiversity data on the Web
Applying computers & the web to the study of biodiversity
Cybertaxonomy
Encyclopedia of Life• A web page for every species
Biodiversity Heritage Library• Digitising biodiversity literature
BiodiversityHeritageLibrary
Scratchpads• Your biodiversity data on the Web
Applying computers & the web to the study of biodiversity
Cybertaxonomy
Encyclopedia of Life• A web page for every species
Biodiversity Heritage Library• Digitising biodiversity literature
BiodiversityHeritageLibrary
Scratchpads• Your biodiversity data on the Web
Applying computers & the web to the study of biodiversity
Encyclopedia of Life (EOL)“A web page for every species”
http://www.eol.org/
• A web page for all 1.8M species
• Multi-institution collaboration
• $50m 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!
Encyclopedia of Life (EOL)“A web page for every species”
• Huge interest- 11.5 million hits in first 5 hours- 500+ press articles- Pages unavailable for first two days!
• First draft 27 Feb. 2008- 24 “exemplar” pages- 30,000 detailed pages (fish & amphib.)- 1 million “stubs” (names & links)
- Growth (needs 1,000 spp. per day)• Much praise but some criticism
- Quality vs. quantity of information- Authoritative “vetting” process- Credit for “authors”
• Nine more years to go- Get more content online- Better tools to engage more people
Biodiversity Heritage Library (BHL)“Digitising biodiversity literature”
• 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• Partnership with “Internet Archive”• Make the contents “findable”
• BHL partnership of 10 Nat. Hist. libraries
Biodiversity Heritage Library (BHL)“Digitising biodiversity literature”
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
Biodiversity Heritage Library (BHL)“Digitising biodiversity literature”
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.
Biodiversity Heritage Library (BHL)“Digitising biodiversity literature”
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.
Biodiversity Heritage Library (BHL)“Digitising biodiversity literature”
2. Extract text (OCR)3. Find keywords
1. Scan
- Taxonomic names- Author names- Citations- Collection data- Morphological data- Descriptions- Identification keys- Illustrations- Photographs
4. Index5. 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.
Biodiversity Heritage Library (BHL)“Digitising biodiversity literature”
• NHM, London- 1 scribe machine- >500k pages- Focus on exceptionally rare text
• Completed to date:- 3,802 periodicals (journals)- 9,181 books- 5.5 million pages (2% of total)
- Copyright (1923)• Challenges
- OCR quality (old fonts)- Better indexing- Foreign language content
http://www.biodiversitylibrary.org/
Cybertaxonomy
Encyclopedia of Life• A Web page for every species
Biodiversity Heritage Library• Digitising biodiversity literature
BiodiversityHeritageLibrary
Scratchpads• Your biodiversity data on the Web
Using computers & the web to study biodiversity
What is a Scratchpad?
Your data1
Published & reviewedon your site
3Uploaded &
tagged
2
“A Website for you & your community”
What is a Scratchpad?
Your data1
Published & reviewedon your site
3Uploaded &
tagged
2
Fast Intuitive Fit for use
“A Website for you & your community”
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: 57Users: 580Pages: 130kSince March 2007
Insect Scratchpads
Building a Scratchpad
Scratchpad applications
European Mosquito Bulletin (ISSN 1460-6127), Phasmid Studies (ISSN 0966-0011)(submission, review, & dissemination of articles)
A multipurpose, flexible technology
eJournals
Scratchpad applications
4th Edition Howard & Moore, Birds of the world(fact checking, data compilation, 2010, funding)
A multipurpose, flexible technology
eBooks
Scratchpad applications
Image galleries
A multipurpose, flexible technology
Nanno fossils, Cockroaches, Stick insects, Flatworms, Grasses, Lichens & many more… (rapid upload, annotation, & display of images)
Integrating EOL, BHL & Scratchpads
Encyclopedia of Life• A web page for every species
Biodiversity Heritage Library• Digitising biodiversity literature
BiodiversityHeritageLibrary
Scratchpads• Your biodiversity data on the Web
Questions?