Science Publishing for the MySpace Generation

Vincent S. Smith

MySpecies & the Encyclopedia of Life

Biodiversity ScienceThe foundation for all biological disciplines

Mission…• Inventory the Earth’s species• Understand their relationships• Create predictive information systems from these data

Data set…• 1.8M described species (10M names)

• 300M pages (over last 250 years)

• 1.5-3B specimens

Staff…• 4-6,000 scientists• 30-40,000 amateurs• Many more citizen scientists?

Biodiversity ScienceThe foundation for all biological disciplines

250 yr progress report…• Up to 87% of life on Earth is still undescribed

• 6% of biodiversity scientists cover 80% of the worlds biodiversity

• At present rates most species will be extinct long before we describe them

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Biodiversity ScienceThe foundation for all biological disciplines

250 yr progress report…• Up to 87% of life on Earth is still undescribed

• 6% of biodiversity scientists cover 80% of the worlds biodiversity

• At present rates most species will be extinct long before we describe them

Problems…• Communities working on biodiversity are highly distributed & fragmented

• So are the data they publish

• The “publication” process for biodiversity data is broken

Most biodiversity (data) is hidden

“Paper Minds”The bottleneck of traditional publication

1,000’s of journals addressinga common set of questions

What is a species? How many species are there? Where are species distributed? How have species distributions changed? How are species related? How have species characters changed? To what extent is are species relationships predictive?

DATA

“Paper Minds”The bottleneck of traditional publication

1,000’s of journals addressinga common set of questions

Mol. Phyl. Evol.21,964 pp. since 2000

Menopon gallinaeNumidicola antennatusAmyrsidea ventralisSomaphantus lusiusMenacanthus stramineusColimenopon urocoliusTrinoton anserinumMeromenopon meropisGruimenopon longumHoazineus armiferusCopocephalum zebraComatomenopon elbeli/elongatumPsittacomenopon poicephalusOdoriphila clayae/phoeniculiArdeiphilus trochioxusCuculiphilus fasciatusCiconiphilus quadripustulatusEomenopon denticulatumPiagetiella bursaepelecaniOsborniella crotophagaeHohorstiella lataNeomenopon pteroclurusMachaerilaemus laticorpus/latifronsAustromenopon crocatumEidmanniella pellucidaHolomenopon brevithoracicumDennyus hirundinisMyrsidea victrixAncistrona vagelliPseudomenopon pilosumBonomiella columbaeChapinia robustaPlegadiphilus threskiornisActornithophilus uniseriatusMEGAMENOPONRediella mirabilisLatumcephalum lesouefi/macropusParaboopia flavaParaheterodoxus insignisBoopia tarsataTherodoxus oweniLaemobothrion maximumRicinus fringillaeTrochiliphagus abdominalisTrochiloecetes rupununiLiposcelis bostrychophilus

What is a species? How many species are there? Where are species distributed? How have species distributions changed? How are species related? How have species characters changed? To what extent is are species relationships predictive?

“Paper Minds”The bottleneck of traditional publication

1,000’s of journals addressinga common set of questions

What is a species? How many species are there? Where are species distributed? How have species distributions changed? How are species related? How have species characters changed? To what extent is are species relationships predictive?

“Species Name”The universal linker

RAW DATA > Logically interconnectedbut presently fragmented by the publication process

Other problems…• Time & money• Audience mismatch• Findability & reusability

Encyclopedia of Life (EOL)“The ultimate life list” - Mitch Leslie, Science

Nothing could possibly go wrong!

http://www.eol.org/

• A web page for every species

• Vision of EO Wilson

• $50m funding (5 years)- MacArthur and Sloan Foundations

• Megascience mashup- First draft 2008, complete 2018!

• Mass collaboration- Science & outreach

EOL Deja Vu

http://ecoport.org/http://www.all-species.org/

http://www.ispecies.org/ http://species.wikimedia.org/

A web page for every species

Vision of EO Wilson

Lots of money

Megascience mashup

Mass collaboration

EOL Content

http://www.biodiversitylibrary.org/

Biodiversity Heritage Library (BHL)

Content managed by

Since May 07: - 323 titles - 3,316 volumes - 1,302,530 pages

“The Internet Archive”

Digitizing the 10 largestNatural History libraries

Since 1469: - 5.4M books - 800,000 monographs - 40,000 journal titles

EOL Content

http://www.biodiversitylibrary.org/

Biodiversity Heritage Library (BHL)

Content managed by

Since May 07: - 323 titles - 3,316 volumes - 1,302,530 pages

“The Internet Archive”

Digitizing the 10 largestNatural History libraries

Since 1469: - 5.4M books - 800,000 monographs - 40,000 journal titles

Are we digitizing the right stuff?

EOL ContentMickey mouse copyright laws

C1923

EOL ContentMost published content cannot be legally

digitized

1923

In Copyright

DOI

Publications on ants

EOL ContentMost published content cannot be legally

digitized

DOI

Publications on ants

1890

In Copyright

(Europe)

Can EOL succeed - define success?

RSScommunity integrative

intuitive

The potential of EOL can only be realized if we rethink “publication”

licensable

MySpeciesA prototype self publication tool for EOL?

A community publication tool to intuitively create, manage and share biodiversity data on the web

http://myspecies.info/

MySpecies

Multi-site CMSconfiguration

A prototype self publication tool for EOL?

Added tools & services

A prototype self publication tool for EOL?MySpecies

MySpeciesA prototype self publication tool for EOL?

Automated site creation

CC LicensingNo content control *

No brandingCitableHelp

MySpecies

… & more

• Birds• Bees• Cockroaches• Corals

• Dung beetles • Fungus gnats• Lice• Milichiid flies

• Mosquitoes • Nanofossils• Polychaetes• Solanaceae

Supporting 22 communities of biologists & counting

http://myspecies.info/SitesList

MySpecies & its successorsA new publishing model for biodiversity data?

Traditional(filter > publish)

• Fractionally “published”• Story telling• Fragmented• Low findability & reusability• Branded• Expensive

Web(publish > filter)

• 100% “published”• Smaller units of information• Findable & reusable• Meaningfully citable (data)• Unbranded• Cheap

MySpecies & its successorsA new publishing model for biodiversity data?

Traditional(filter > publish)

• Fractionally “published”• Story telling• Fragmented• Low findability & reusability• Branded• Expensive

Web(publish > filter)

• 100% “published”• Smaller units of information• Findable & reusable• Meaningfully citable (data)• Unbranded• Cheap

But,What aboutpeer review!

MySpecies & Peer ReviewHow can we provide quality assurance?

Web(publish > filter)

Data algorithmically checked

Peer used or ignored

Traditional(filter > publish)

Data ignored / stories checked

MySpecies & Peer ReviewHow can we provide quality assurance?

Web(publish > filter)

Data algorithmically checked

Peer used or ignored

Traditional(filter > publish)

Data ignored / stories checked

Questions?