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?